
@Article{AKP+10,
  author    = {Albrethsen, Jakob and Knol, Jaco C. and Piersma, Sander R. and Pham, Thang V. and de Wit, Meike and Mongera, Sandra and Carvalho, Beatriz and Verheul, Henk M. W. and Fijneman, Remond J. A. and Meijer, Gerrit A. and Jimenez, Connie R.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{S}ubnuclear proteomics in colorectal cancer: {I}dentification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression},
  year      = {2010},
  volume    = {9},
  number    = {5},
  pages     = {988--1005},
  doi       = {10.1074/mcp.M900546-MCP200},
}

@Article{BPV+11,
  author    = {Besson, Damien and Pavageau, Aude-H\'el\`ene and Valo, Isabelle and Bourreau, Anthony and B\'elanger, Audrey and Eymerit-Morin, Caroline and Mouli\`ere, Alice and Chassevent, Agn\`es and Boisdron-Celle, Michelle and Morel, Alain and Solassol, Jer\^ome and Campone, Mario and Gamelin, Erick and Barr\'e, Benjamin and Coqueret, Olivier and Guette, Catherine},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{A} quantitative proteomic approach of the different stages of colorectal cancer establishes {OLFM}4 as a new nonmetastatic tumor marker},
  year      = {2011},
  volume    = {10},
  number    = {12},
  pages     = {M111.009712},
  doi       = {10.1074/mcp.M111.009712},
}

@Article{BSA+15,
  author    = {Bousquet, Paula A. and Sandvik, Joe Alexander and Arntzen, Magnus {\O}. and Jeppesen Edin, Nina F. and Christoffersen, Stine and Krengel, Ute and Pettersen, Erik O. and Thiede, Bernd},
  journal   = {International Journal of Proteomics},
  title     = {{H}ypoxia strongly affects mitochondrial ribosomal proteins and translocases, as shown by quantitative proteomics of {H}e{L}a cells},
  year      = {2015},
  volume    = {2015},
  pages     = {678527},
  doi       = {10.1155/2015/678527},
}

@Article{CIR+10,
  author    = {Cha, Sangwon and Imielinski, Marcin B. and Rejtar, Tomas and Richardson, Elizabeth A. and Thakur, Dipak and Sgroi, Dennis C. and Karger, Barry L.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {\emph{In situ} proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: {A}nnotation by protein set enrichment analysis and gene ontology},
  year      = {2010},
  volume    = {9},
  number    = {11},
  pages     = {2529--2544},
  doi       = {10.1074/mcp.M110.000398},
}

@Article{CHN+08,
  author    = {Chaerkady, Raghothama and Harsha, H. C. and Nalli, Anuradha and Gucek, Marjan and Vivekanandan, Perumal and Akhtar, Javed and Cole, Robert N. and Simmers, Jessica and Schulick, Richard D. and Singh, Sujay and Torbenson, Michael and Pandey, Akhilesh and Thuluvath, Paul J.},
  journal   = {Journal of Proteome Research},
  title     = {{A} quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma},
  year      = {2008},
  number    = {10},
  pages     = {4289--4298},
  volume    = {7},
  doi       = {10.1021/pr800197z},
}

@Article{CZL+16,
  author    = {Chen, Chen and Zhang, Li-Guo and Liu, Jian and Han, Hui and Chen, Ning and Yao, An-Liang and Kang, Shao-San and Gao, Wei-Xing and Shen, Hong and Zhang, Long-Jun and Li, Ya-Peng and Cao, Feng-Hong and Li, Zhi-Guo},
  journal   = {OncoTargets and Therapy},
  title     = {{B}ioinformatics analysis of differentially expressed proteins in prostate cancer based on proteomics data},
  year      = {2016},
  pages     = {1545--1557},
  volume    = {9},
  doi       = {10.2147/OTT.S98807},
}

@Article{DCH+14,
  author    = {Djidja, Marie-Claude and Chang, Joan and Hadjiprocopis, Andreas and Schmich, Fabian and Sinclair, John and Mr\v{s}nik, Martina and Schoof, Erwin M. and Barker, Holly E. and Linding, Rune and Jørgensen, Claus and Erler, Janine T.},
  journal   = {Journal of Proteome Research},
  title     = {{I}dentification of hypoxia-regulated proteins using {MALDI}-mass spectrometry imaging combined with quantitative proteomics},
  year      = {2014},
  number    = {5},
  pages     = {2297--2313},
  volume    = {13},
  doi       = {10.1021/pr401056c},
}

@Article{GTM+12,
  author    = {Gormley, Michael and Tchafa, Alimatou and Meng, Rong and Zhong, Zhijiu and Quong, Andrew A.},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteomic profiling of infiltrating ductal carcinoma reveals increased cellular interactions with tissue microenvironment},
  year      = {2012},
  number    = {4},
  pages     = {2236--2246},
  volume    = {11},
  doi       = {10.1021/pr201018y},
}

@Article{HXS+06,
  author    = {Han, Yu-Hui and Xia, Li and Song, Li-Ping and Zheng, Ying and Chen, Wen-Li and Zhang, Lei and Huang, Ying and Chen, Guo-Qiang and Wang, Li-Shun},
  journal   = {Proteomics},
  title     = {{C}omparative proteomic analysis of hypoxia-treated and untreated human leukemic {U}937 cells},
  year      = {2006},
  number    = {11},
  pages     = {3262--3274},
  volume    = {6},
  doi       = {10.1002/pmic.200500754},
}

@Article{HTP+11,
  author    = {Hill, Jennifer J. and Tremblay, Tammy-Lynn and Pen, Ally and Li, Jie and Robotham, Anna C. and Lenferink, Anne E. G. and Wang, Edwin and O’Connor-McCourt, Maureen and Kelly, John F.},
  journal   = {Journal of Proteome Research},
  title     = {{I}dentification of vascular breast tumor markers by laser capture microdissection and label-free {LC}-{MS}},
  year      = {2011},
  number    = {5},
  pages     = {2479--2493},
  volume    = {10},
  doi       = {10.1021/pr101267k},
}

@Article{JCF+11,
  author    = {Jankova, Lucy and Chan, Charles and Fung, Caroline L. S. and Song, Xiaomin and Kwun, Sun Y. and Cowley, Mark J. and Kaplan, Warren and Dent, Owen F. and Bokey, Elie L. and Chapuis, Pierre H. and Baker, Mark S. and Robertson, Graham R. and Clarke, Stephen J. and Molloy, Mark P.},
  journal   = {Molecular Biosystems},
  title     = {{P}roteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using i{TRAQ} mass spectrometry},
  year      = {2011},
  number    = {11},
  pages     = {2997--3005},
  volume    = {7},
  doi       = {10.1039/C1MB05236E},
}

@Article{JKMF10,
  author    = {Jimenez, Connie R. and Knol, Jaco C. and Meijer, Gerrit A. and Fijneman, Remond J. A.},
  journal   = {Journal of Proteomics},
  title     = {{P}roteomics of colorectal cancer: {O}verview of discovery studies and identification of commonly identified cancer-associated proteins and candidate {CRC} serum markers},
  year      = {2010},
  number    = {10},
  pages     = {1873--1895},
  volume    = {73},
  doi       = {10.1016/j.jprot.2010.06.004},
}

@Article{KPB+10,
  author    = {Khan, Amjad P. and Poisson, Laila M. and Bhat, Vadiraja B. and Fermin, Damian and Zhao, Rong and Kalyana-Sundaram, Shanker and Michailidis, George and Nesvizhskii, Alexey I. and Omenn, Gilbert S. and Chinnaiyan, Arul M. and Sreekumar, Arun},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{Q}uantitative proteomic profiling of prostate cancer reveals a role for mi{R}-128 in prostate cancer},
  year      = {2010},
  volume    = {9},
  number    = {2},
  pages     = {298--312},
  doi       = {10.1074/mcp.M900159-MCP200},
}

@Article{KWA+14,
  author    = {Knol, Jaco C. and de Wit, Meike and Albrethsen, Jakob and Piersma, Sander R. and Pham, Thang V. and Mongera, Sandra and Carvalho, Beatriz and Fijneman, Remond J. A. and Meijer, Gerrit A. and Jim\'enez, Connie R.},
  journal   = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
  title     = {{P}roteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues},
  year      = {2014},
  number    = {5},
  pages     = {1034--1043},
  volume    = {1844},
  doi       = {10.1016/j.bbapap.2013.12.006},
}

@Article{LLL+13,
  author    = {Liang, Jin-long and Li, Si-jie and Liu, Xiang-guo and Li, Wan-feng and Hao, Dong-yun and Fan, Zhi-min},
  journal   = {Chemical Research in Chinese Universities},
  title     = {{Q}uantitative proteomic studies on {TNBC} in premenopausal patients},
  year      = {2013},
  number    = {3},
  pages     = {500--505},
  volume    = {29},
  doi       = {10.1007/s40242-013-2497-9},
}

@Article{MVC+12,
  author    = {McMahon, K. M. and Volpato, M. and Chi, H. Y. and Musiwaro, P. and Poterlowicz, K. and Peng, Y. and Scally, A. J. and Patterson, L. H. and Phillips, R. M. and Sutton, C. W.},
  journal   = {Journal of Proteome Research},
  title     = {{C}haracterization of changes in the proteome in different regions of 3{D} multicell tumor spheroids},
  year      = {2012},
  number    = {5},
  pages     = {2863--2875},
  volume    = {11},
  doi       = {10.1021/pr2012472},
}

@Article{MBK+13,
  author    = {Megger, Dominik A. and Bracht, Thilo and Kohl, Michael and Ahrens, Maike and Naboulsi, Wael and Weber, Frank and Hoffmann, Andreas-Claudius and Stephan, Christian and Kuhlmann, Katja and Eisenacher, Martin and Schlaak, Jörg F. and Baba, Hideo A. and Meyer, Helmut E. and Sitek, Barbara},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {Proteomic differences between hepatocellular carcinoma and nontumorous liver tissue investigated by a combined gel-based and label-free quantitative proteomics study},
  year      = {2013},
  number    = {7},
  pages     = {2006--2020},
  volume    = {12},
  doi       = {10.1074/mcp.M113.028027},
}

@Article{MHG+12,
  author    = {Morrison, Brian J. and Hastie, Marcus L. and Grewal, Yadveer S. and Bruce, Zara C. and Schmidt, Chris and Reynolds, Brent A. and Gorman, Jeffrey J. and Lopez, J. Alejandro},
  journal   = {PLOS One},
  title     = {{P}roteomic comparison of {MCF}-7 tumoursphere and monolayer cultures},
  year      = {2012},
  number    = {12},
  pages     = {e52692},
  volume    = {7},
  doi       = {10.1371/journal.pone.0052692},
}

@Article{PPH+14,
  author    = {Panis, Carolina and Pizzatti, Luciana and Herrera, Ana Cristina and Corrêa, Stephany and Binato, Renata and Abdelhay, Eliana},
  journal   = {Journal of Proteome Research},
  title     = {{L}abel-free proteomic analysis of breast cancer molecular subtypes},
  year      = {2014},
  number    = {11},
  pages     = {4752--4772},
  volume    = {13},
  doi       = {10.1021/pr500676x},
}

@Article{PBR+16,
  author    = {Pozniak, Yair and Balint-Lahat, Nora and Rudolph, Jan Daniel and Lindskog, Cecilia and Katzir, Rotem and Avivi, Camilla and Pontén, Fredrik and Ruppin, Eytan and Barshack, Iris and Geiger, Tamar},
  journal   = {Cell Systems},
  title     = {{S}ystem-wide clinical proteomics of breast cancer reveals global remodeling of tissue homeostasis},
  year      = {2016},
  number    = {3},
  pages     = {172--184},
  volume    = {2},
  doi       = {10.1016/j.cels.2016.02.001},
}

@Article{RKP+14,
  author    = {Rajcevic, Uros and Knol, Jaco and Piersma, Sander and Bougnaud, Sebastien and Fack, Fred and Sundlisaeter, Eirik and Sondenaa, Karl and Myklebust, Reidar and Pham, Thang and Niclou, Simone and Jimenez, Connie},
  journal   = {Proteome Science},
  title     = {{C}olorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture},
  year      = {2014},
  number    = {1},
  pages     = {39},
  volume    = {12},
  doi       = {10.1186/1477-5956-12-39},
}

@Article{RHD+13,
  author    = {Ren, Yan and Hao, Piliang and Dutta, Bamaprasad and Cheow, Esther Sok Hwee and Sim, Kae Hwan and Gan, Chee Sian and Lim, Sai Kiang and Sze, Siu Kwan},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{H}ypoxia modulates {A}431 cellular pathways association to tumor radioresistance and enhanced migration revealed by comprehensive proteomic and functional studies},
  year      = {2013},
  volume    = {12},
  number    = {2},
  pages     = {485--498},
  doi       = {10.1074/mcp.M112.018325},
}

@Article{STK+15,
  author    = {Sethi, Manveen K. and Thaysen-Andersen, Morten and Kim, Hoguen and Park, Cheol Keun and Baker, Mark S. and Packer, Nicolle H. and Paik, Young-Ki and Hancock, William S. and Fanayan, Susan},
  journal   = {Journal of Proteomics},
  title     = {{Q}uantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in {CRC} progression and metastasis},
  year      = {2015},
  pages     = {54--67},
  volume    = {126},
  doi       = {10.1016/j.jprot.2015.05.037},
}

@Article{SRS+13,
  author    = {Shaheed, Sadr-ul and Rustogi, Nitin and Scally, Andrew and Wilson, Julie and Thygesen, Helene and Loizidou, Maria A. and Hadjisavvas, Andreas and Hanby, Andrew and Speirs, Valerie and Loadman, Paul and Linforth, Richard and Kyriacou, Kyriacos and Sutton, Chris W.},
  journal   = {Journal of Proteome Research},
  title     = {{I}dentification of stage-specific breast markers using quantitative proteomics},
  year      = {2013},
  number    = {12},
  pages     = {5696--5708},
  volume    = {12},
  doi       = {10.1021/pr400662k},
}

@Article{SHHS11,
  author    = {Shi, Hongjun and Hood, Kylie A. and Hayes, Mark T. and Stubbs, Richard S.},
  journal   = {Journal of Proteomics},
  title     = {{P}roteomic analysis of advanced colorectal cancer by laser capture microdissection and two-dimensional difference gel electrophoresis},
  year      = {2011},
  number    = {2},
  pages     = {339--351},
  volume    = {75},
  doi       = {10.1016/j.jprot.2011.07.025},
}

@Article{SRG+10,
  author    = {Sutton, Chris W. and Rustogi, Nitin and Gurkan, Cemal and Scally, Andrew and Loizidou, Maria A. and Hadjisavvas, Andreas and Kyriacou, Kyriacos},
  journal   = {Journal of Proteome Research},
  title     = {{Q}uantitative proteomic profiling of matched normal and tumor breast tissues},
  year      = {2010},
  number    = {8},
  pages     = {3891--3902},
  volume    = {9},
  doi       = {10.1021/pr100113a},
}

@Article{UNS+14,
  author    = {Uzozie, Anuli and Nanni, Paolo and Staiano, Teresa and Grossmann, Jonas and Barkow-Oesterreicher, Simon and Shay, Jerry W. and Tiwari, Amit and Buffoli, Federico and Laczko, Endre and Marra, Giancarlo},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{S}orbitol dehydrogenase overexpression and other aspects of dysregulated protein expression in human precancerous colorectal neoplasms: {A} quantitative proteomics study},
  year      = {2014},
  volume    = {13},
  number    = {5},
  pages     = {1198--1218},
  doi       = {10.1074/mcp.M113.035105},
}

@Article{WDO+15,
  author    = {Wi\'sniewski, Jacek R. and Du\'s-Szachniewicz, Kamila and Ostasiewicz, Pawe{\l} and Zi\'o{\l}kowski, Piotr and Rakus, Dariusz and Mann, Matthias},
  journal   = {Journal of Proteome Research},
  title     = {{A}bsolute proteome analysis of colorectal mucosa, adenoma, and cancer reveals drastic changes in fatty acid metabolism and plasma membrane transporters},
  year      = {2015},
  number    = {9},
  pages     = {4005--4018},
  volume    = {14},
  doi       = {10.1021/acs.jproteome.5b00523},
}

@Article{WOD+12,
  author    = {Wi\'sniewski, Jacek R. and Ostasiewicz, Pawe{\l} and Du\'s, Kamila and Zieli\'nska, Dorota F. and Gnad, Florian and Mann, Matthias},
  journal   = {Molecular Systems Biology},
  title     = {{E}xtensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma},
  year      = {2012},
  number    = {1},
  pages     = {611},
  volume    = {8},
  doi       = {10.1038/msb.2012.44},
}

@Article{KKL+12,
  author    = {Kim, Hye-Jung and Kang, Un-Beom and Lee, Hanna and Jung, Ji-Han and Lee, Seung-Taek and Yu, Myeong-Hee and Kim, Hoguen and Lee, Cheolju},
  journal   = {Journal of Proteomics},
  title     = {{P}rofiling of differentially expressed proteins in stage {IV} colorectal cancers with good and poor outcomes},
  year      = {2012},
  number    = {10},
  pages     = {2983--2997},
  volume    = {75},
  doi       = {10.1016/j.jprot.2011.12.002},
}

@Article{KYK+12,
  author    = {Kang, Un-Beom and Yeom, Jeonghun and Kim, Hye-Jung and Kim, Hoguen and Lee, Cheolju},
  journal   = {Journal of Proteomics},
  title     = {{E}xpression profiling of more than 3500 proteins of {MSS}-type colorectal cancer by stable isotope labeling and mass spectrometry},
  year      = {2012},
  number    = {10},
  pages     = {3050--3062},
  volume    = {75},
  doi       = {10.1016/j.jprot.2011.11.021},
}

@Article{XZC+10,
  author    = {Xie, Li-Qi and Zhao, Chao and Cai, San-Jun and Xu, Ye and Huang, Li-Yong and Bian, Jia-Shen and Shen, Cheng-Pin and Lu, Hao-Jie and Yang, Peng-Yuan},
  journal   = {Journal of Proteome Research},
  title     = {{N}ovel proteomic strategy reveal combined $\alpha_1$ antitrypsin and cathepsin {D} as biomarkers for colorectal cancer early screening},
  year      = {2010},
  number    = {9},
  pages     = {4701--4709},
  volume    = {9},
  doi       = {10.1021/pr100406z},
}

@Article{PGT+16,
  author    = {Pendharkar, Namita and Gajbhiye, Akshada and Taunk, Khushman and RoyChoudhury, Sourav and Dhali, Snigdha and Seal, Shubhendu and Mane, Anupama and Abhang, Subodhini and Santra, Manas K. and Chaudhury, Koel and Rapole, Srikanth},
  journal   = {Journal of Proteomics},
  title     = {{Q}uantitative tissue proteomic investigation of invasive ductal carcinoma of breast with luminal {B} {HER}2 positive and {HER}2 enriched subtypes towards potential diagnostic and therapeutic biomarkers},
  year      = {2016},
  pages     = {112--130},
  volume    = {132},
  doi       = {10.1016/j.jprot.2015.11.024},
}

@Article{WKP+14,
  author    = {de Wit, Meike and Kant, Huub and Piersma, Sander R. and Pham, Thang V. and Mongera, Sandra and van Berkel, Maaike P. A. and Boven, Epie and Pontén, Fredrik and Meijer, Gerrit A. and Jimenez, Connie R. and Fijneman, Remond J. A.},
  journal   = {Journal of Proteomics},
  title     = {{C}olorectal cancer candidate biomarkers identified by tissue secretome proteome profiling},
  year      = {2014},
  pages     = {26--39},
  volume    = {99},
  doi       = {10.1016/j.jprot.2014.01.001},
}

@Article{NMB+16,
  author    = {Naboulsi, Wael and Megger, Dominik A. and Bracht, Thilo and Kohl, Michael and Turewicz, Michael and Eisenacher, Martin and Voss, Don Marvin and Schlaak, Jörg F. and Hoffmann, Andreas-Claudius and Weber, Frank and Baba, Hideo A. and Meyer, Helmut E. and Sitek, Barbara},
  journal   = {Journal of Proteome Research},
  title     = {Quantitative tissue proteomics analysis reveals versican as potential biomarker for early-stage hepatocellular carcinoma},
  year      = {2016},
  number    = {1},
  pages     = {38--47},
  volume    = {15},
  doi       = {10.1021/acs.jproteome.5b00420},
}

@Article{ZLH+14,
  author    = {Zhang, Xuede and Li, Wei and Hou, Yanli and Niu, Zequn and Zhong, Yujie and Zhang, Yuping and Yang, Shuanying},
  journal   = {American Journal of Translational Research},
  title     = {{C}omparative membrane proteomic analysis between lung adenocarcinoma and normal tissue by i{TRAQ} labeling mass spectrometry},
  year      = {2014},
  number    = {3},
  pages     = {267--280},
  volume    = {6},
  url       = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058308/},
}

@Article{WLL+13,
  author    = {Wang, Wan-Sheng and Liu, Xiao-Hui and Liu, Ling-Xiao and Lou, Wen-Hui and Jin, Da-Yong and Yang, Peng-Yuan and Wang, Xiao-Lin},
  journal   = {Journal of Proteomics},
  title     = {i{TRAQ}-based quantitative proteomics reveals myoferlin as a novel prognostic predictor in pancreatic adenocarcinoma},
  year      = {2013},
  pages     = {453--465},
  volume    = {91},
  doi       = {10.1016/j.jprot.2013.06.032},
}

@Article{ZYS+10,
  author    = {Zhang, Yanbin and Ye, Yingjiang and Shen, Danhua and Jiang, Kewei and Zhang, Hui and Sun, Wei and Zhang, Jiyang and Xu, Feng and Cui, Zhirong and Wang, Shan},
  journal   = {Cancer Science},
  title     = {{I}dentification of transgelin-2 as a biomarker of colorectal cancer by laser capture microdissection and quantitative proteome analysis},
  year      = {2010},
  number    = {2},
  pages     = {523--529},
  volume    = {101},
  doi       = {10.1111/j.1349-7006.2009.01424.x},
}

@Article{FWH+13,
  author    = {Fuhrmann, Dominik Christian and Wittig, Ilka and Heide, Heinrich and Dehne, Nathalie and Brüne, Bernhard},
  journal   = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
  title     = {{C}hronic hypoxia alters mitochondrial composition in human macrophages},
  year      = {2013},
  number    = {12},
  pages     = {2750--2760},
  volume    = {1834},
  doi       = {10.1016/j.bbapap.2013.09.023},
}

@Article{RSE+16,
  author    = {Riis, Simone and Stensballe, Allan and Emmersen, Jeppe and Pennisi, Cristian Pablo and Birkelund, Svend and Zachar, Vladimir and Fink, Trine},
  journal   = {Stem Cell Research \& Therapy},
  title     = {{M}ass spectrometry analysis of adipose-derived stem cells reveals a significant effect of hypoxia on pathways regulating extracellular matrix},
  year      = {2016},
  number    = {1},
  pages     = {1--14},
  volume    = {7},
  doi       = {10.1186/s13287-016-0310-7},
}

@Article{WRK+14,
  author    = {Wrzesinski, Krzysztof and Rogowska-Wrzesinska, Adelina and Kanlaya, Rattiyaporn and Borkowski, Kamil and Schw\"ammle, Veit and Dai, Jie and Joensen, Kira Eyd and Wojdyla, Katarzyna and Carvalho, Vasco Botelho and Fey, Stephen J.},
  journal   = {PLOS One},
  title     = {{T}he cultural divide: {E}xponential growth in classical 2{D} and metabolic equilibrium in 3{D} environments},
  year      = {2014},
  number    = {9},
  pages     = {e106973},
  volume    = {9},
  doi       = {10.1371/journal.pone.0106973},
}

@Article{MRK+11,
  author    = {Mikula, Michal and Rubel, Tymon and Karczmarski, Jakub and Goryca, Krzysztof and Dadlez, Michal and Ostrowski, Jerzy},
  journal   = {Functional and Integrative Genomics},
  title     = {{I}ntegrating proteomic and transcriptomic high-throughput surveys for search of new biomarkers of colon tumors},
  year      = {2011},
  number    = {2},
  pages     = {215--224},
  volume    = {11},
  doi       = {10.1007/s10142-010-0200-5},
}

@Article{WTK+08,
  author    = {Watanabe, Makoto and Takemasa, Ichiro and Kawaguchi, Naomasa and Miyake, Masakazu and Nishimura, Noriko and Matsubara, Toshiya and Matsuo, Ei-ichi and Sekimoto, Mitsugu and Nagai, Katsuya and Matsuura, Nariaki and Monden, Morito and Nishimura, Osamu},
  journal   = {Proteomics: Clinical Applications},
  title     = {{A}n application of the 2-nitrobenzenesulfenyl method to proteomic profiling of human colorectal carcinoma: {A} novel approach for biomarker discovery},
  year      = {2008},
  number    = {6},
  pages     = {925--935},
  volume    = {2},
  doi       = {10.1002/prca.200780111},
}

@Article{YLZ+12,
  author    = {Yao, Ling and Lao, Weifeng and Zhang, Yan and Tang, Xiaorong and Hu, Xiaotong and He, Chao and Hu, Xiaofang and Xu, Lisa X.},
  journal   = {Journal of Proteome Research},
  title     = {{I}dentification of {EFEMP}2 as a serum biomarker for the early detection of colorectal cancer with lectin affinity capture assisted secretome analysis of cultured fresh tissues},
  year      = {2012},
  number    = {6},
  pages     = {3281--3294},
  volume    = {11},
  doi       = {10.1021/pr300020p},
}

@Article{BMJ+11,
  author    = {van den Beucken, Twan and Magagnin, Michael G. and Jutten, Barry and Seigneuric, Renaud and Lambin, Philippe and Koritzinsky, Marianne and Wouters, Bradly G.},
  journal   = {Radiotherapy and Oncology},
  title     = {{T}ranslational control is a major contributor to hypoxia induced gene expression},
  year      = {2011},
  number    = {3},
  pages     = {379--384},
  volume    = {99},
  doi       = {10.1016/j.radonc.2011.05.058},
}

@Article{LCS16,
  author    = {Lai, Ming-Chih and Chang, Chiao-May and Sun, H. Sunny},
  journal   = {PLOS One},
  title     = {{H}ypoxia induces autophagy through translational up-regulation of lysosomal proteins in human colon cancer cells},
  year      = {2016},
  number    = {4},
  pages     = {e0153627},
  volume    = {11},
  doi       = {10.1371/journal.pone.0153627},
}

@Article{LRS+14,
  author    = {Xin Li and Yan Ren and Vitaly Sorokin and Kian Keong Poh and Hee Hwa Ho and Chuen Neng Lee and Dominique de Kleijn and Sai Kiang Lim and James P. Tam and Siu Kwan Sze},
  journal   = {Journal of Proteomics},
  title     = {{Q}uantitative profiling of the rat heart myoblast secretome reveals differential responses to hypoxia and re-oxygenation stress},
  year      = {2014},
  pages     = {138--149},
  volume    = {98},
  doi       = {10.1016/j.jprot.2013.12.025},
}

@Article{HWA+16,
  author    = {Ho, J. J. David and Wang, Miling and Audas, Timothy E. and Kwon, Deukwoo and Carlsson, Steven K. and Timpano, Sara and Evagelou, Sonia L. and Brothers, Shaun and Gonzalgo, Mark L. and Krieger, Jonathan R. and Chen, Steven and Uniacke, James and Lee, Stephen},
  journal   = {Cell Reports},
  title     = {{S}ystemic reprogramming of translation efficiencies on oxygen stimulus},
  year      = {2016},
  number    = {6},
  pages     = {1293--1300},
  volume    = {14},
  doi       = {10.1016/j.celrep.2016.01.036},
}

@Article{PHL+16,
  author    = {Peng, Fang and Huang, Ying and Li, Mao-Yu and Li, Guo-Qing and Huang, Hui-Chao and Guan, Rui and Chen, Zhu-Chu and Liang, Song-Ping and Chen, Yong-Heng},
  journal   = {World Journal of Gastroenterology},
  title     = {{D}issecting characteristics and dynamics of differentially expressed proteins during multistage carcinogenesis of human colorectal cancer},
  year      = {2016},
  number    = {18},
  pages     = {4515--4528},
  volume    = {22},
  doi       = {10.3748/wjg.v22.i18.4515},
}

@Article{LPL+16,
  author    = {Li, Maoyu and Peng, Fang and Li, Guoqing and Fu, Yang and Huang, Ying and Chen, Zhuchu and Chen, Yongheng},
  journal   = {Oncotarget},
  title     = {{P}roteomic analysis of stromal proteins in different stages of colorectal cancer establishes {T}enascin-{C} as a stromal biomarker for colorectal cancer metastasis},
  year      = {2016},
  number    = {24},
  pages     = {37226--37237},
  volume    = {7},
  doi       = {10.18632/oncotarget.9362},
}

@Article{LXM+16,
  author    = {Liu, Xing and Xu, Yanli and Meng, Qian and Zheng, Qingqing and Wu, Jianhong and Wang, Chen and Jia, Weiping and Figeys, Daniel and Chang, Ying and Zhou, Hu},
  journal   = {Biochemical and Biophysical Research Communications},
  title     = {{P}roteomic analysis of minute amount of colonic biopsies by enteroscopy sampling},
  year      = {2016},
  number    = {4},
  pages     = {286--292},
  volume    = {476},
  doi       = {10.1016/j.bbrc.2016.05.114},
}

@Article{MCZ+13,
  author    = {Mu, Yibing and Chen, Yongheng and Zhang, Guiying and Zhan, Xianquan and Li, Yuanyuan and Liu, Ting and Li, Guoqing and Li, Maoyu and Xiao, Zhefeng and Gong, Xiaoxiang and Chen, Zhuchu},
  journal   = {Electrophoresis},
  title     = {{I}dentification of stromal differentially expressed proteins in the colon carcinoma by quantitative proteomics},
  year      = {2013},
  number    = {11},
  pages     = {1679--1692},
  volume    = {34},
  doi       = {10.1002/elps.201200596},
}

@Article{KKC+16,
  author    = {Kuo, Kung-Kai and Kuo, Chao-Jen and Chiu, Chiang-Yen and Liang, Shih-Shin and Huang, Chun-Hao and Chi, Shu-Wen and Tsai, Kun-Bow and Chen, Chiao-Yun and Hsi, Edward and Cheng, Kuang-Hung and Chiou, Shyh-Horng},
  journal   = {Pancreas},
  title     = {{Q}uantitative proteomic analysis of differentially expressed protein profiles involved in pancreatic ductal adenocarcinoma},
  year      = {2016},
  volume    = {45},
  number    = {1},
  pages     = {71--83},
  doi       = {10.1097/MPA.0000000000000388},
}

@Article{IWT+16,
  author    = {Diego Iglesias-Gato and Pernilla Wikstr\"om and Stefka Tyanova and Charlotte Lavallee and Elin Thysell and Jessica Carlsson and Christina H\"aggl\"of and J\"urgen Cox and Ove Andr\'en and P\"ar Stattin and Lars Egevad and Anders Widmark and Anders Bjartell and Colin C. Collins and Anders Bergh and Tamar Geiger and Matthias Mann and Amilcar Flores-Morales},
  journal   = {European Urology},
  title     = {{T}he proteome of primary prostate cancer},
  year      = {2016},
  number    = {5},
  pages     = {942--952},
  volume    = {69},
  doi       = {10.1016/j.eururo.2015.10.053},
}

@Article{CBW+11,
  author    = {Cifani, Paolo and Bendz, Maria and Wårell, Kristofer and Hansson, Karin and Levander, Fredrik and Sandin, Marianne and Krogh, Morten and Ovenberger, Marie and Fredlund, Erik and Vaapil, Marica and Pietras, Alexander and Påhlman, Sven and James, Peter},
  journal   = {Journal of Proteome Research},
  title     = {{H}unting for protein markers of hypoxia by combining plasma membrane enrichment with a new approach to membrane protein analysis},
  year      = {2011},
  number    = {4},
  pages     = {1645--1656},
  volume    = {10},
  doi       = {10.1021/pr100982j},
}

@Article{HHH+16,
  author    = {Hsu, Chiung-Hung and Hsu, Chia-Wei and Hsueh, Chuen and Wang, Chih-Liang and Wu, Yi-Cheng and Wu, Chih-Ching and Liu, Chin-Ching and Yu, Jau-Song and Chang, Yu-Sun and Yu, Chia-Jung},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{I}dentification and characterization of potential biomarkers by quantitative tissue proteomics of primary lung adenocarcinoma},
  year      = {2016},
  volume    = {15},
  number    = {7},
  pages     = {2396--2410},
  doi       = {10.1074/mcp.M115.057026},
}

@Article{DPL+10,
  author    = {Datta, Arnab and Park, Jung Eun and Li, Xin and Zhang, Huoming and Ho, Zhi Shan and Heese, Klaus and Lim, Sai Kiang and Tam, James P. and Sze, Siu Kwan},
  journal   = {Journal of Proteome Research},
  title     = {{P}henotyping of an \emph{in vitro} model of ischemic penumbra by i{TRAQ}-based shotgun quantitative proteomics},
  year      = {2010},
  number    = {1},
  pages     = {472--484},
  volume    = {9},
  doi       = {10.1021/pr900829h},
}

@Article{LAR+12,
  author    = {Li, Xin and Arslan, Fatih and Ren, Yan and Adav, Sunil S. and Poh, Kian Keong and Sorokin, Vitaly and Lee, Chuen Neng and de Kleijn, Dominique and Lim, Sai Kiang and Sze, Siu Kwan},
  journal   = {Journal of Proteome Research},
  title     = {{M}etabolic adaptation to a disruption in oxygen supply during myocardial ischemia and reperfusion is underpinned by temporal and quantitative changes in the cardiac proteome},
  year      = {2012},
  number    = {4},
  pages     = {2331--2346},
  volume    = {11},
  doi       = {10.1021/pr201025m},
}

@Article{PTD+10,
  author    = {Park, Jung Eun and Tan, Hon Sen and Datta, Arnab and Lai, Ruenn Chai and Zhang, Huoming and Meng, Wei and Lim, Sai Kiang and Sze, Siu Kwan},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{H}ypoxic tumor cell modulates its microenvironment to enhance angiogenic and metastatic potential by secretion of proteins and exosomes},
  year      = {2010},
  volume    = {9},
  number    = {6},
  pages     = {1085--1099},
  doi       = {10.1074/mcp.M900381-MCP200},
}

@Article{VTMF13,
  author    = {Villeneuve, Lance and Tiede, LeAnn M. and Morsey, Brenda and Fox, Howard S.},
  journal   = {Journal of Proteome Research},
  title     = {{Q}uantitative proteomics reveals oxygen-dependent changes in neuronal mitochondria affecting function and sensitivity to rotenone},
  year      = {2013},
  number    = {10},
  pages     = {4599--4606},
  volume    = {12},
  doi       = {10.1021/pr400758d},
}

@Article{DYL+14,
  author    = {Dutta, Bamaprasad and Yan, Ren and Lim, Sai Kiang and Tam, James P. and Sze, Siu Kwan},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{Q}uantitative profiling of chromatome dynamics reveals a novel role for {HP}1{BP}3 in hypoxia-induced oncogenesis},
  year      = {2014},
  volume    = {13},
  number    = {12},
  pages     = {3236--3249},
  doi       = {10.1074/mcp.M114.038232},
}

@Article{YLL+12,
  author    = {Yan, Xu and Lan-Qin, Cao and Long-Yu, Jin and Zhu-Chu, Chen and Gu-Qing, Zeng and Can-E, Tang and Guo-Qing, Li and Chao-Jun, Duan and Fang, Peng and Zhi-Qiang, Xiao and Cui, Li},
  journal   = {Journal of Biomedicine and Biotechnology},
  title     = {{Q}uantitative proteomic study of human lung squamous carcinoma and normal bronchial epithelial acquired by laser capture microdissection},
  year      = {2012},
  volume    = {2012},
  pages     = {510418},
  doi       = {10.1155/2012/510418},
}

@Article{BRA+10,
  author    = {Blankley, Richard T. and Robinson, Nicola J. and Aplin, John D. and Crocker, Ian P. and Gaskell, Simon J. and Whetton, Anthony D. and Baker, Philip N. and Myers, Jenny E.},
  journal   = {Reproductive Sciences},
  title     = {{A} gel-free quantitative proteomics analysis of factors released from hypoxic-conditioned placentae},
  year      = {2010},
  volume    = {17},
  number    = {3},
  pages     = {247--257},
  doi       = {10.1177/1933719109351320},
}

@Article{ISI+14,
  author    = {Iuga, Cristina and Seicean, Andrada and Iancu, Cornel and Buiga, Rareş and Sappa, Praveen K. and Völker, Uwe and Hammer, Elke},
  journal   = {Proteomics},
  title     = {{P}roteomic identification of potential prognostic biomarkers in resectable pancreatic ductal adenocarcinoma},
  year      = {2014},
  number    = {7-8},
  pages     = {945--955},
  volume    = {14},
  doi       = {10.1002/pmic.201300402},
}

@Article{MLC+11,
  author    = {McKinney, Kimberly Q. and Lee, Yong-Yook and Choi, Hyun-Su and Groseclose, Gale and Iannitti, David A. and Martinie, John B. and Russo, Mark W. and Lundgren, Deborah H. and Han, David K. and Bonkovsky, Herbert L. and Hwang, Sun-Il},
  journal   = {Journal of Proteomics},
  title     = {{D}iscovery of putative pancreatic cancer biomarkers using subcellular proteomics},
  year      = {2011},
  number    = {1},
  pages     = {79--88},
  volume    = {74},
  doi       = {10.1016/j.jprot.2010.08.006},
}

@Article{PCS+11,
  author    = {Pan, Sheng and Chen, Ru and Stevens, Tyler and Bronner, Mary P. and May, Damon and Tamura, Yasuko and McIntosh, Martin W. and Brentnall, Teresa A.},
  journal   = {PLOS One},
  title     = {{P}roteomics portrait of archival lesions of chronic pancreatitis},
  year      = {2011},
  number    = {11},
  pages     = {e27574},
  volume    = {6},
  doi       = {10.1371/journal.pone.0027574},
}

@Article{CTZ+09,
  author    = {Cui, Yazhou and Tian, Mei and Zong, Meijuan and Teng, Mujian and Chen, Yu and Lu, Jun and Jiang, Jinbo and Liu, Xiaoyong and Han, Jinxiang},
  journal   = {Pancreatology},
  title     = {{P}roteomic analysis of pancreatic ductal adenocarcinoma compared with normal adjacent pancreatic tissue and pancreatic benign cystadenoma},
  year      = {2009},
  number    = {1-2},
  pages     = {89--98},
  volume    = {9},
  doi       = {10.1159/000178879},
}

@Article{CGB+05,
  author    = {Crnogorac-Jurcevic, Tatjana and Gangeswaran, Rathi and Bhakta, Vipul and Capurso, Gabriele and Lattimore, Samuel and Akada, Masanori and Sunamura, Makoto and Prime, Wendy and Campbell, Fiona and Brentnall, Teresa A. and Costello, Eithne and Neoptolemos, John and Lemoine, Nicholas R.},
  journal   = {Gastroenterology},
  title     = {{P}roteomic analysis of chronic pancreatitis and pancreatic adenocarcinoma},
  year      = {2005},
  number    = {5},
  pages     = {1454--1463},
  volume    = {129},
  doi       = {10.1053/j.gastro.2005.08.012},
}

@Article{KBK+12,
  author    = {Kojima, Kyoko and Bowersock, Gregory J. and Kojima, Chinatsu and Klug, Christopher A. and Grizzle, William E. and Mobley, James A.},
  journal   = {Proteomics},
  title     = {{V}alidation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human},
  year      = {2012},
  number    = {22},
  pages     = {3393--3402},
  volume    = {12},
  doi       = {10.1002/pmic.201100663},
}

@Article{KPC+13,
  author    = {Kosanam, Hari and Prassas, Ioannis and Chrystoja, Caitlin C. and Soleas, Ireena and Chan, Alison and Dimitromanolakis, Apostolos and Blasutig, Ivan M. and Rückert, Felix and Gruetzmann, Robert and Pilarsky, Christian and Maekawa, Masato and Brand, Randall and Diamandis, Eleftherios P.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{L}aminin, gamma 2 ({LAMC}2): {A} promising new putative pancreatic cancer biomarker identified by proteomic analysis of pancreatic adenocarcinoma tissues},
  year      = {2013},
  number    = {10},
  pages     = {2820--2832},
  volume    = {12},
  doi       = {10.1074/mcp.M112.023507},
}

@Article{ZNWL13,
  author    = {Zhu, Jianhui and Nie, Song and Wu, Jing and Lubman, David M.},
  journal   = {Journal of Proteome Research},
  title     = {{T}arget proteomic profiling of frozen pancreatic {CD}24+ adenocarcinoma tissues by immuno-laser capture microdissection and nano-{LC}–{MS}/{MS}},
  year      = {2013},
  number    = {6},
  pages     = {2791--2804},
  volume    = {12},
  doi       = {10.1021/pr400139c},
}

@Article{PKB+13,
  author    = {Paulo, Joao A. and Kadiyala, Vivek and Brizard, Scott and Banks, Peter A. and Steen, Hanno and Conwell, Darwin L.},
  journal   = {Journal of the Pancreas},
  title     = {{A} proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer},
  year      = {2013},
  number    = {4},
  pages     = {405--414},
  volume    = {14},
  doi       = {10.6092/1590-8577/1508},
}

@Article{CYD+05,
  author    = {Chen, Ru and Yi, Eugene C. and Donohoe, Samuel and Pan, Sheng and Eng, Jimmy and Cooke, Kelly and Crispin, David A. and Lane, Zhaoli and Goodlett, David R. and Bronner, Mary P. and Aebersold, Ruedi and Brentnall, Teresa A.},
  journal   = {Gastroenterology},
  title     = {{P}ancreatic cancer proteome: {T}he proteins that underlie invasion, metastasis, and immunologic escape},
  year      = {2005},
  number    = {4},
  pages     = {1187--1197},
  volume    = {129},
  doi       = {10.1053/j.gastro.2005.08.001},
}

@Article{KHO+13,
  author    = {Kawahara, Takeo and Hotta, Naoe and Ozawa, Yukiko and Kato, Seiichi and Kano, Keiko and Yokoyama, Yukihiro and Nagino, Masato and Takahashi, Takashi and Yanagisawa, Kiyoshi},
  journal   = {PLOS One},
  title     = {{Q}uantitative proteomic profiling identifies {DPYSL}3 as pancreatic ductal adenocarcinoma-associated molecule that regulates cell adhesion and migration by stabilization of focal adhesion complex},
  year      = {2013},
  number    = {12},
  pages     = {e79654},
  volume    = {8},
  doi       = {10.1371/journal.pone.0079654},
}

@Article{TMW+11,
  author    = {Turtoi, Andrei and Musmeci, Davide and Wang, Yinghong and Dumont, Bruno and Somja, Joan and Bevilacqua, Generoso and De Pauw, Edwin and Delvenne, Philippe and Castronovo, Vincent},
  journal   = {Journal of Proteome Research},
  title     = {{I}dentification of novel accessible proteins bearing diagnostic and therapeutic potential in human pancreatic ductal adenocarcinoma},
  year      = {2011},
  number    = {9},
  pages     = {4302--4313},
  volume    = {10},
  doi       = {10.1021/pr200527z},
}

@Article{CBP+07,
  author    = {Chen, Ru and Brentnall, Teresa A. and Pan, Sheng and Cooke, Kelly and Moyes, Kara White and Lane, Zhaoli and Crispin, David A. and Goodlett, David R. and Aebersold, Ruedi and Bronner, Mary P.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{Q}uantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer},
  year      = {2007},
  volume    = {6},
  number    = {8},
  pages     = {1331--1342},
  doi       = {10.1074/mcp.M700072-MCP200},
}

@Article{LHE+04,
  author    = {Lu, ZhaoHui and Hu, LiPing and Evers, Stefan and Chen, Jie and Shen, Yan},
  journal   = {Proteomics},
  title     = {{D}ifferential expression profiling of human pancreatic adenocarcinoma and healthy pancreatic tissue},
  year      = {2004},
  number    = {12},
  pages     = {3975--3988},
  volume    = {4},
  doi       = {10.1002/pmic.200300863},
}

@Article{KKG+12,
  author        = {Kocharunchitt, Chawalit and King, Thea and Gobius, Kari and Bowman, John P. and Ross, Tom},
  journal       = {Molecular \& Cellular Proteomics},
  title         = {{I}ntegrated transcriptomic and proteomic analysis of the physiological response of \emph{{E}scherichia coli} {O}157:{H}7 {S}akai to steady-state conditions of cold and water activity stress},
  year          = {2012},
  volume        = {11},
  number        = {1},
  pages         = {M111.009019},
  doi           = {10.1074/mcp.M111.009019},
}

@Article{PW08,
  author    = {Pham, Trong Khoa and Wright, Phillip C.},
  journal   = {Journal of Proteome Research},
  title     = {{T}he proteomic response of \emph{{S}accharomyces cerevisiae} in very high glucose conditions with amino acid supplementation},
  year      = {2008},
  number    = {11},
  pages     = {4766--4774},
  volume    = {7},
  doi       = {10.1021/pr800331s},
}

@Article{YDZ+15,
  author    = {Yang, Li-Bo and Dai, Xiao-Meng and Zheng, Zhi-Yong and Zhu, Li and Zhan, Xiao-Bei and Lin, Chi-Chung},
  journal   = {Journal of Microbiology and Biotechnology},
  title     = {{P}roteomic analysis of erythritol-producing \emph{{Y}arrowia lipolytica} from glycerol in response to osmotic pressure},
  year      = {2015},
  number    = {7},
  pages     = {1056--1069},
  volume    = {25},
  doi       = {10.4014/jmb.1412.12026},
}

@Article{DAA+05,
  author    = {Dihazi, Hassan and Asif, Abdul R. and Agarwal, Nitin K. and Doncheva, Yuliana and Müller, Gerhard A.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{P}roteomic analysis of cellular response to osmotic stress in thick ascending limb of {H}enle’s loop ({TALH}) cells},
  year      = {2005},
  number    = {10},
  pages     = {1445--1458},
  volume    = {4},
  doi       = {10.1074/mcp.M400184-MCP200},
}

@Article{GSC14,
  author    = {Giardina, Bennett J. and Stanley, Bruce A. and Chiang, Hui-Ling},
  journal   = {Proteome Science},
  title     = {{G}lucose induces rapid changes in the secretome of \emph{{S}accharomyces cerevisiae}},
  year      = {2014},
  number    = {1},
  pages     = {9},
  volume    = {12},
  doi       = {10.1186/1477-5956-12-9},
}

@Article{CCC+12,
  author    = {Chen, You-Hsuan and Chen, Jing-Yi and Chen, Yi-Wen and Lin, Szu-Ting and Chan, Hong-Lin},
  journal   = {Molecular Biosystems},
  title     = {{H}igh glucose-induced proteome alterations in retinal pigmented epithelium cells and its possible relevance to diabetic retinopathy},
  year      = {2012},
  number    = {12},
  pages     = {3107--3124},
  volume    = {8},
  doi       = {10.1039/C2MB25331C},
}

@Article{CCCC13,
  author    = {Jing-Yi Chen and Hsiu-Chuan Chou and You-Hsuan Chen and Hong-Lin Chan},
  journal   = {Journal of Nutritional Biochemistry},
  title     = {{H}igh glucose-induced proteome alterations in hepatocytes and its possible relevance to diabetic liver disease},
  year      = {2013},
  number    = {11},
  pages     = {1889--1910},
  volume    = {24},
  doi       = {10.1016/j.jnutbio.2013.05.006},
}

@Article{LDB+15,
  author    = {Liu, Zhenke and Dai, Shujia and Bones, Jonathan and Ray, Somak and Cha, Sangwon and Karger, Barry L. and Li, Jingyi Jessica and Wilson, Lee and Hinckle, Greg and Rossomando, Anthony},
  journal   = {Biotechnology Progress},
  title     = {{A} quantitative proteomic analysis of cellular responses to high glucose media in {C}hinese hamster ovary cells},
  year      = {2015},
  number    = {4},
  pages     = {1026--1038},
  volume    = {31},
  doi       = {10.1002/btpr.2090},
}

@Article{WCM+09,
  author    = {Waanders, Leonie F. and Chwalek, Karolina and Monetti, Mara and Kumar, Chanchal and Lammert, Eckhard and Mann, Matthias},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {{Q}uantitative proteomic analysis of single pancreatic islets},
  year      = {2009},
  number    = {45},
  pages     = {18902--18907},
  volume    = {106},
  doi       = {10.1073/pnas.0908351106},
}

@Article{OBBH11,
  author    = {Oswald, Elizabeth S. and Brown, Lewis M. and Bulinski, J. Chloë and Hung, Clark T.},
  journal   = {Journal of Proteome Research},
  title     = {{L}abel-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment},
  year      = {2011},
  number    = {7},
  pages     = {3050--3059},
  volume    = {10},
  doi       = {10.1021/pr200030v},
}

@Article{CLG+15,
  author    = {Chen, Liyan and Li, Jing and Guo, Tiannan and Ghosh, Sujoy and Koh, Siew Kwan and Tian, Dechao and Zhang, Liang and Jia, Deyong and Beuerman, Roger W. and Aebersold, Ruedi and Chan, Eric Chun Yong and Zhou, Lei},
  journal   = {Journal of Proteome Research},
  title     = {{G}lobal metabonomic and proteomic analysis of human conjunctival epithelial cells ({IOBA}-{NHC}) in response to hyperosmotic stress},
  year      = {2015},
  number    = {9},
  pages     = {3982--3995},
  volume    = {14},
  doi       = {10.1021/acs.jproteome.5b00443},
}

@Article{KLB+15,
  author    = {Kohler, Christian and Louren\c{c}o, Rog\'erio F. and Bernhardt, J\"org and Albrecht, Dirk and Sch\"uler, Julia and Hecker, Michael and Gomes, Suely L.},
  journal   = {BMC Microbiology},
  title     = {{A} comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive $\alpha$-proteobacterium},
  year      = {2015},
  number    = {1},
  pages     = {1--15},
  volume    = {15},
  doi       = {10.1186/s12866-015-0404-x},
}

@Article{ZLZ+16,
  author    = {Zhang, Yao and Li, Yanchang and Zhang, Yongguang and Wang, Zhiqiang and Zhao, Mingzhi and Su, Na and Zhang, Tao and Chen, Lingsheng and Wei, Wei and Luo, Jing and Zhou, Yanxia and Xu, Yongru and Xu, Ping and Li, Wenjun and Tao, Yong},
  journal   = {Journal of Proteome Research},
  title     = {{Q}uantitative proteomics reveals membrane protein-mediated hypersaline sensitivity and adaptation in halophilic \emph{{N}ocardiopsis xinjiangensis}},
  year      = {2016},
  number    = {1},
  pages     = {68--85},
  volume    = {15},
  doi       = {10.1021/acs.jproteome.5b00526},
}

@Article{GSB+14,
  author    = {Groessl, Michael and Slany, Astrid and Bileck, Andrea and Gloessmann, Kerstin and Kreutz, Dominique and Jaeger, Walter and Pfeiler, Georg and Gerner, Christopher},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteome profiling of breast cancer biopsies reveals a wound healing signature of cancer-associated fibroblasts},
  year      = {2014},
  number    = {11},
  pages     = {4773--4782},
  volume    = {13},
  doi       = {10.1021/pr500727h},
}

@Article{SBB+06,
  author    = {Stockwin, Luke H. and Blonder, Josip and Bumke, Maja A. and Lucas, David A. and Chan, King C. and Conrads, Thomas P. and Issaq, Haleem J. and Veenstra, Timothy D. and Newton, Dianne L. and Rybak, Susanna M.},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteomic analysis of plasma membrane from hypoxia-adapted malignant melanoma},
  year      = {2006},
  number    = {11},
  pages     = {2996--3007},
  volume    = {5},
  doi       = {10.1021/pr0601739},
}

@Article{XWS+14,
  author    = {Xu, Bo and Wang, Fangjun and Song, Chunxia and Sun, Zhen and Cheng, Kai and Tan, Yexiong and Wang, Hongyang and Zou, Hanfa},
  journal   = {Journal of Proteome Research},
  title     = {{L}arge-scale proteome quantification of hepatocellular carcinoma tissues by a three-dimensional liquid chromatography strategy integrated with sample preparation},
  year      = {2014},
  number    = {8},
  pages     = {3645--3654},
  volume    = {13},
  doi       = {10.1021/pr500200s},
}

@Article{YLW+16,
  author    = {Yue, Xiaoshan and Lukowski, Jessica K. and Weaver, Eric M. and Skube, Susan B. and Hummon, Amanda B.},
  journal   = {Journal of Proteome Research},
  title     = {{Q}uantitative proteomic and phosphoproteomic comparison of 2{D} and 3{D} colon cancer cell culture models},
  year      = {2016},
  number    = {12},
  pages     = {4265--4276},
  volume    = {15},
  doi       = {10.1021/acs.jproteome.6b00342},
}

@Article{KOK+13,
  author    = {Kazuya Kimura and Hidenori Ojima and Daisuke Kubota and Marimu Sakumoto and Yukiko Nakamura and Tsuyoshi Tomonaga and Tmoo Kosuge and Tadashi Kondo},
  journal   = {Journal of Proteomics},
  title     = {Proteomic identification of the macrophage-capping protein as a protein contributing to the malignant features of hepatocellular carcinoma},
  year      = {2013},
  pages     = {362--373},
  volume    = {78},
  doi       = {10.1016/j.jprot.2012.10.004},
}

@Article{LMG+11,
  author    = {Lee, Yong-Yook and McKinney, Kimberly Q. and Ghosh, Sriparna and Iannitti, David A. and Martinie, John B. and Caballes, F. Ryan and Russo, Mark W. and Ahrens, William A. and Lundgren, Deborah H. and Han, David K. and Bonkovsky, Herbert L. and Hwang, Sun-Il},
  journal   = {Journal of Proteome Research},
  title     = {Subcellular tissue proteomics of hepatocellular carcinoma for molecular signature discovery},
  year      = {2011},
  number    = {11},
  pages     = {5070--5083},
  volume    = {10},
  doi       = {10.1021/pr2005204},
}

@Article{WLL+13a,
  author    = {Wan-Sheng Wang and Xiao-Hui Liu and Ling-Xiao Liu and Da-Yong Jin and Peng-Yuan Yang and Xiao-Lin Wang},
  journal   = {Journal of Proteomics},
  title     = {{I}dentification of proteins implicated in the development of pancreatic cancer-associated diabetes mellitus by i{TRAQ}-based quantitative proteomics},
  year      = {2013},
  pages     = {52--60},
  volume    = {84},
  doi       = {10.1016/j.jprot.2013.03.031},
}

@Article{FTR+10,
  author    = {Fränzel, Benjamin and Trötschel, Christian and Rückert, Christian and Kalinowski, Jörn and Poetsch, Ansgar and Wolters, Dirk Andreas},
  journal   = {Proteomics},
  title     = {{A}daptation of \emph{{C}orynebacterium glutamicum} to salt-stress conditions},
  year      = {2010},
  number    = {3},
  pages     = {445--457},
  volume    = {10},
  doi       = {10.1002/pmic.200900482},
}

@Article{RBP+16,
  author    = {Leandro Nascimento da Silva Rodrigues and Wesley de Almeida Brito and Ana Flávia Alves Parente and Simone Schneider Weber and Alexandre Melo Bailão and Luciana Casaletti and Clayton Luiz Borges and Célia Maria de Almeida Soares},
  journal   = {Fungal Genetics and Biology},
  title     = {{O}smotic stress adaptation of \emph{{P}aracoccidioides lutzii}, {P}b01, monitored by proteomics},
  year      = {2016},
  pages     = {13--23},
  volume    = {95},
  doi       = {10.1016/j.fgb.2016.08.001},
}

@Article{TSZ+13,
  author    = {Tse, William Ka Fai and Sun, Jin and Zhang, Huoming and Law, Alice Yu Sheung and Yeung, Bonnie Ho Yee and Chow, Sheung Ching and Qiu, Jian-Wen and Wong, Chris Kong Chu},
  journal   = {Journal of Proteomics},
  title     = {{T}ranscriptomic and i{TRAQ} proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the {J}apanese eel (\emph{{A}nguilla japonica})},
  year      = {2013},
  pages     = {81--94},
  volume    = {89},
  doi       = {10.1016/j.jprot.2013.05.026},
}

@Article{XCJ+16,
  author    = {Xu, Zhong-Wei and Chen, Xi and Jin, Xiao-Han and Meng, Xiang-Yan and Zhou, Xin and Fan, Feng-Xu and Mao, Shi-Yun and Wang, Yue and Zhang, Wen-Cheng and Shan, Na-Na and Li, Yu-Ming and Xu, Rui-Cheng},
  journal   = {Journal of Proteomics},
  title     = {{SILAC}-based proteomic analysis reveals that salidroside antagonizes cobalt chloride-induced hypoxic effects by restoring the tricarboxylic acid cycle in cardiomyocytes},
  year      = {2016},
  pages     = {211--220},
  volume    = {130},
  doi       = {10.1016/j.jprot.2015.09.028},
}

@Article{LHT+04,
  author    = {Li, Chen and Hong, Yi and Tan, Ye-Xiong and Zhou, Hu and Ai, Jian-Hua and Li, Su-Jun and Zhang, Lei and Xia, Qi-Chang and Wu, Jia-Rui and Wang, Hong-Yang and Zeng, Rong},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry},
  year      = {2004},
  number    = {4},
  pages     = {399--409},
  volume    = {3},
  doi       = {10.1074/mcp.M300133-MCP200},
}

@Article{NBM+16,
  author    = {Wael Naboulsi and Thilo Bracht and Dominik A. Megger and Henning Reis and Maike Ahrens and Michael Turewicz and Martin Eisenacher and Stephanie Tautges and Ali E. Canbay and Helmut E. Meyer and Frank Weber and Hideo A. Baba and Barbara Sitek},
  journal   = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
  title     = {Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation},
  year      = {2016},
  number    = {11},
  pages     = {1579--1585},
  volume    = {1864},
  doi       = {10.1016/j.bbapap.2016.08.005},
}

@Article{RPM+15,
  author    = {Henning Reis and Carolin Pütter and Dominik A. Megger and Thilo Bracht and Frank Weber and Andreas-C. Hoffmann and Stefanie Bertram and Jeremias Wohlschläger and Sascha Hagemann and Martin Eisenacher and André Scherag and Jörg F. Schlaak and Ali Canbay and Helmut E. Meyer and Barbara Sitek and Hideo A. Baba},
  journal   = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
  title     = {{A} structured proteomic approach identifies 14-3-3{S}igma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors},
  year      = {2015},
  number    = {6},
  pages     = {641--650},
  volume    = {1854},
  doi       = {10.1016/j.bbapap.2014.10.024},
}

@Article{SXS+07,
  author    = {Sun, Wei and Xing, Baocai and Sun, Yi and Du, Xiaojuan and Lu, Min and Hao, Chunyi and Lu, Zhuang and Mi, Wei and Wu, Songfeng and Wei, Handong and Gao, Xue and Zhu, Yunping and Jiang, Ying and Qian, Xiaohong and He, Fuchu},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{P}roteome analysis of hepatocellular carcinoma by two-dimensional difference gel electrophoresis: {N}ovel protein markers in hepatocellular carcinoma tissues},
  year      = {2007},
  number    = {10},
  pages     = {1798--1808},
  volume    = {6},
  doi       = {10.1074/mcp.M600449-MCP200},
}

@Article{CVJ+15,
  author    = {Campone, Mario and Valo, Isabelle and Jézéquel, Pascal and Moreau, Marie and Boissard, Alice and Campion, Loic and Loussouarn, Delphine and Verriele, Véronique and Coqueret, Olivier and Guette, Catherine},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{P}rediction of recurrence and survival for triple-negative breast cancer ({TNBC}) by a protein signature in tissue samples},
  year      = {2015},
  volume    = {14},
  number    = {11},
  pages     = {2936--2946},
  doi       = {10.1074/mcp.M115.048967},
}

@Article{YKK+14,
  author    = {Yoon, Jong Hyuk and Kim, Jaeyoon and Kim, Kyung Lock and Kim, Do-Hyeon and Jung, Sun-Ju and Lee, Hyeongjoo and Ghim, Jaewang and Kim, Dayea and Park, Jong Bae and Ryu, Sung Ho and Lee, Taehoon G.},
  journal   = {Proteomics},
  title     = {{P}roteomic analysis of hypoxia-induced {U}373{MG} glioma secretome reveals novel hypoxia-dependent migration factors},
  year      = {2014},
  number    = {12},
  pages     = {1494--1502},
  volume    = {14},
  doi       = {10.1002/pmic.201300554},
}

@Article{CTW+17,
  author    = {Alba Cristobal and Henk W.P. van den Toorn and Marc van de Wetering and Hans Clevers and Albert J.R. Heck and Shabaz Mohammed},
  journal   = {Cell Reports},
  title     = {{P}ersonalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer},
  year      = {2017},
  number    = {1},
  pages     = {263--274},
  volume    = {18},
  doi       = {10.1016/j.celrep.2016.12.016},
}

@Article{BST+17,
  author    = {Braakman, René B.H. and Stingl, Christoph and Tilanus-Linthorst, Madeleine M.A. and Deurzen, Carolien H.M. and Timmermans, Mieke A.M. and Smid, Marcel and Foekens, John A. and Luider, Theo M. and Martens, John W.M. and Umar, Arzu},
  journal   = {Proteomics},
  title     = {{P}roteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation},
  year      = {2017},
  number    = {5},
  pages     = {1600213},
  volume    = {17},
  doi       = {10.1002/pmic.201600213},
}

@Article{LXC+06,
  author    = {Li, Cui and Xiao, Zhiqiang and Chen, Zhuchu and Zhang, Xiaopeng and Li, JianLing and Wu, Xiaoying and Li, Xinying and Yi, Hong and Li, Maoyu and Zhu, Guo and Liang, Songping},
  journal   = {Proteomics},
  title     = {{P}roteome analysis of human lung squamous carcinoma},
  year      = {2006},
  number    = {2},
  pages     = {547--558},
  volume    = {6},
  doi       = {10.1002/pmic.200500256},
}

@Article{WLL+17,
  author    = {Yingchao Wang and Hongzhi Liu and Dong Liang and Yao Huang and Yongyi Zeng and Xiaohua Xing and Jiangbao Xia and Minjie Lin and Xiao Han and Naishun Liao and Xiaolong Liu and Jingfeng Liu},
  journal   = {Journal of Proteomics},
  title     = {{R}eveal the molecular signatures of hepatocellular carcinoma with different sizes by i{TRAQ} based quantitative proteomics},
  year      = {2017},
  pages     = {230--241},
  volume    = {150},
  doi       = {10.1016/j.jprot.2016.09.008},
}

@Article{LRL+12,
  author    = {Li, Chen and Ruan, Hong-Qiang and Liu, Yan-Sheng and Xu, Meng-Jie and Dai, Jie and Sheng, Quan-Hu and Tan, Ye-Xiong and Yao, Zhen-Zhen and Wang, Hong-Yang and Wu, Jia-Rui and Zeng, Rong},
  journal   = {Journal of Proteome Research},
  title     = {Quantitative proteomics reveal up-regulated protein expression of the {SET} complex associated with hepatocellular carcinoma},
  year      = {2012},
  number    = {2},
  pages     = {871--885},
  volume    = {11},
  doi       = {10.1021/pr2006999},
}

@Article{FGP+16,
  author    = {Fahrmann, Johannes F. and Grapov, Dmitry and Phinney, Brett S. and Stroble, Carol and DeFelice, Brian C. and Rom, William and Gandara, David R. and Zhang, Yanhong and Fiehn, Oliver and Pass, Harvey and Miyamoto, Suzanne},
  journal   = {Clinical Proteomics},
  title     = {{P}roteomic profiling of lung adenocarcinoma indicates heightened {DNA} repair, antioxidant mechanisms and identifies {LASP}1 as a potential negative predictor of survival},
  year      = {2016},
  number    = {1},
  pages     = {31},
  volume    = {13},
  doi       = {10.1186/s12014-016-9132-y},
}

@Article{AMG+08,
  author    = {Alldridge, Louise and Metodieva, Gergana and Greenwood, Christina and Al-Janabi, Khalid and Thwaites, Laura and Sauven, Paul and Metodiev, Metodi},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteome profiling of breast tumors by gel electrophoresis and nanoscale electrospray ionization mass spectrometry},
  year      = {2008},
  number    = {4},
  pages     = {1458--1469},
  volume    = {7},
  doi       = {10.1021/pr7007829},
}

@Article{JCP+16,
  author    = {Hongwei Jin and Xiao Cheng and Yihua Pei and Jianguo Fu and Zhi Lyu and Huifang Peng and Qin Yao and Yu Jiang and Lianzhong Luo and Huiqin Zhuo},
  journal   = {Journal of Proteomics},
  title     = {{I}dentification and verification of transgelin-2 as a potential biomarker of tumor-derived lung-cancer endothelial cells by comparative proteomics},
  year      = {2016},
  pages     = {77--88},
  volume    = {136},
  doi       = {10.1016/j.jprot.2015.12.012},
}

@Article{LRB+09,
  author    = {Leuko, Stefan and Raftery, Mark J. and Burns, Brendan P. and Walter, Malcolm R. and Neilan, Brett A.},
  journal   = {Journal of Proteome Research},
  title     = {{G}lobal protein-level responses of \emph{{H}alobacterium salinarum} {NRC}-1 to prolonged changes in external sodium chloride concentrations},
  year      = {2009},
  number    = {5},
  pages     = {2218--2225},
  volume    = {8},
  doi       = {10.1021/pr800663c},
}

@Article{TGD18,
  author    = {Toelle, Regine C. and Gaggioli, Cedric and Dengjel, Joern},
  journal   = {Journal of Proteome Research},
  title     = {{T}hree-dimensional cell culture conditions affect the proteome of cancer-associated fibroblasts},
  year      = {2018},
  number    = {8},
  pages     = {2780--2789},
  volume    = {17},
  doi       = {10.1021/acs.jproteome.8b00237},
}

@Article{YCC+17,
  author    = {Yang, Shuang and Chen, Lijun and Chan, Daniel W. and Li, Qing Kay and Zhang, Hui},
  journal   = {Clinical Proteomics},
  title     = {{P}rotein signatures of molecular pathways in non-small cell lung carcinoma ({NSCLC}): comparison of glycoproteomics and global proteomics},
  year      = {2017},
  pages     = {31},
  volume    = {14},
  doi       = {10.1186/s12014-017-9166-9},
}

@Article{LLC+19,
  author    = {Liu, Chenchen and Liu, Ying and Chen, Lei and Zhang, Mingjun and Li, Wei and Cheng, Huaidong and Zhang, Bo},
  journal   = {Breast Cancer},
  title     = {{Q}uantitative proteome and lysine succinylome analyses provide insights into metabolic regulation in breast cancer},
  year      = {2019},
  number    = {1},
  pages     = {93--105},
  volume    = {26},
  doi       = {10.1007/s12282-018-0893-1},
}

@Article{TOT+19,
  author    = {Lilla Turiák and Oliver Ozohanics and Gábor Tóth and András Ács and Ágnes Révész and Károly Vékey and András Telekes and László Drahos},
  journal   = {Journal of Proteomics},
  title     = {{H}igh sensitivity proteomics of prostate cancer tissue microarrays to discriminate between healthy and cancerous tissue},
  year      = {2019},
  pages     = {82--91},
  volume    = {197},
  doi       = {10.1016/j.jprot.2018.11.009},
}

@Article{TZD+18,
  author    = {Tang, Wei and Zhou, Ming and Dorsey, Tiffany H. and Prieto, DaRue A. and Wang, Xin W. and Ruppin, Eytan and Veenstra, Timothy D. and Ambs, Stefan},
  journal   = {Genome Medicine},
  title     = {{I}ntegrated proteotranscriptomics of breast cancer reveals globally increased protein-m{RNA} concordance associated with subtypes and survival},
  year      = {2018},
  number    = {1},
  pages     = {94},
  volume    = {10},
  doi       = {10.1186/s13073-018-0602-x},
}

@Article{YKK+13,
  author    = {Yu, Jiyoung and Kim, Kyunggon and Kang, MeeJoo and Kim, Hyunsoo and Kim, Sun Whe and Jang, Jin-Young and Kim, Youngsoo},
  journal   = {Biotechnology and Bioprocess Engineering},
  title     = {{D}evelopment of candidate biomarkers for pancreatic ductal adenocarcinoma using multiple reaction monitoring},
  year      = {2013},
  number    = {5},
  pages     = {1038--1047},
  volume    = {18},
  doi       = {10.1007/s12257-013-0421-2},
}

@Article{MAN+18,
  author    = {Martiny, Patricia Borba and Alcoba, Diego Duarte and Neto, Brasil Silva and Carvalho, Paulo Costa and Brum, Ilma Simoni},
  journal   = {Journal of Applied Biomedicine},
  title     = {{A} proteomic glimpse into the oncogenesis of prostate cancer},
  year      = {2018},
  number    = {4},
  pages     = {328--336},
  volume    = {16},
  doi       = {10.1016/j.jab.2018.05.003},
}

@Article{LAJ+18,
  author    = {Latonen, Leena and Afyounian, Ebrahim and Jylha, Antti and Nattinen, Janika and Aapola, Ulla and Annala, Matti and Kivinummi, Kati K. and Tammela, Teuvo T. L. and Beuerman, Roger W. and Uusitalo, Hannu and Nykter, Matti and Visakorpi, Tapio},
  journal   = {Nature Communications},
  title     = {{I}ntegrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression},
  year      = {2018},
  pages     = {1176},
  volume    = {9},
  doi       = {10.1038/s41467-018-03573-6},
}

@Article{LCS+14,
  author    = {Liu, Yansheng and Chen, Jing and Sethi, Atul and Li, Qing K. and Chen, Lijun and Collins, Ben and Gillet, Ludovic C. J. and Wollscheid, Bernd and Zhang, Hui and Aebersold, Ruedi},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{G}lycoproteomic analysis of prostate cancer tissues by {SWATH} mass spectrometry discovers {N}-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness},
  year      = {2014},
  number    = {7},
  pages     = {1753--1768},
  volume    = {13},
  doi       = {10.1074/mcp.M114.038273},
}

@Article{DWW+18,
  author    = {Dorayappan, Kalpana Deepa Priya and Wanner, Ross and Wallbillich, John J. and Saini, Uksha and Zingarelli, Roman and Suarez, Adrian A. and Cohn, David E. and Selvendiran, Karuppaiyah},
  journal   = {Oncogene},
  title     = {{H}ypoxia-induced exosomes contribute to a more aggressive and chemoresistant ovarian cancer phenotype: a novel mechanism linking {STAT}3/{R}ab proteins},
  year      = {2018},
  number    = {28},
  pages     = {3806--3821},
  volume    = {37},
  doi       = {10.1038/s41388-018-0189-0},
}

@Article{LWT+14,
  author    = {Li, Lei and Wei, Yuhong and To, Christine and Zhu, Chang-Qi and Tong, Jiefei and Pham, Nhu-An and Taylor, Paul and Ignatchenko, Vladimir and Ignatchenko, Alex and Zhang, Wen and Wang, Dennis and Yanagawa, Naoki and Li, Ming and Pintilie, Melania and Liu, Geoffrey and Muthuswamy, Lakshmi and Shepherd, Frances A. and Tsao, Ming Sound and Kislinger, Thomas and Moran, Michael F.},
  journal   = {Nature Communications},
  title     = {{I}ntegrated {O}mic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact},
  year      = {2014},
  pages     = {5469},
  volume    = {5},
  doi       = {10.1038/ncomms6469},
}

@Article{FGW+17,
  author    = {Fahrmann, Johannes F. and Grapov, Dmitry and Wanichthanarak, Kwanjeera and DeFelice, Brian C. and Salemi, Michelle R. and Rom, William N. and Gandara, David R. and Phinney, Brett S. and Fiehn, Oliver and Pass, Harvey and Miyamoto, Suzanne},
  journal   = {Carcinogenesis},
  title     = {{I}ntegrated metabolomics and proteomics highlight altered nicotinamide and polyamine pathways in lung adenocarcinoma},
  year      = {2017},
  number    = {3},
  pages     = {271--280},
  volume    = {38},
  doi       = {10.1093/carcin/bgw205},
}

@Article{KHA+12,
  author    = {Kikuchi, Takefumi and Hassanein, Mohamed and Amann, Joseph M. and Liu, Qinfeng and Slebos, Robbert J. C. and Rahman, S. M. Jamshedur and Kaufman, Jacob M. and Zhang, Xueqiong and Hoeksema, Megan D. and Harris, Bradford K. and Li, Ming and Shyr, Yu and Gonzalez, Adriana L. and Zimmerman, Lisa J. and Liebler, Daniel C. and Massion, Pierre P. and Carbone, David P.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{I}n-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers},
  year      = {2012},
  number    = {10},
  pages     = {916--932},
  volume    = {11},
  doi       = {10.1074/mcp.M111.015370},
}

@Article{SFS+17,
  author    = {Stewart, Paul A. and Fang, Bin and Slebos, Robbert J. C. and Zhang, Guolin and Borne, Adam L. and Fellows, Katherine and Teer, Jamie K. and Chen, Y. Ann and Welsh, Eric and Eschrich, Steven A. and Haura, Eric B. and Koomen, John M.},
  journal   = {Proteomics},
  title     = {{R}elative protein quantification and accessible biology in lung tumor proteomes from four {LC}-{MS}/{MS} discovery platforms},
  year      = {2017},
  volume    = {17},
  number    = {6},
  pages     = {1600300},
  doi       = {10.1002/pmic.201600300},
}

@Article{LLY+14,
  author    = {Lihong, Hao and Linlin, Gong and Yiping, Guo and Yang, Song and Xiaoyu, Qi and Zhuzhu, Guan and Xiaohan, Yang and Xin, Zhou and Liyan, Xue and Shujuan, Shao},
  journal   = {PLOS One},
  title     = {{P}roteomics approaches for identification of tumor relevant protein targets in pulmonary squamous cell carcinoma by 2{D}-{DIGE}-{MS}},
  year      = {2014},
  number    = {4},
  pages     = {e95121},
  volume    = {9},
  doi       = {10.1371/journal.pone.0095121},
}

@Article{GBH+18,
  author    = {Greenhough, Alexander and Bagley, Clare and Heesom, Kate J and Gurevich, David B and Gay, David and Bond, Mark and Collard, Tracey J and Paraskeva, Chris and Martin, Paul and Sansom, Owen J and Malik, Karim and Williams, Ann C},
  journal   = {EMBO Molecular Medicine},
  title     = {{C}ancer cell adaptation to hypoxia involves a {HIF}-{GPRC}5{A}-{YAP} axis},
  year      = {2018},
  number    = {11},
  pages     = {e8699},
  volume    = {10},
  doi       = {10.15252/emmm.201708699},
}

@Article{TLB+16,
  author    = {Tenzer, Stefan and Leidinger, Petra and Backes, Christina and Huwer, Hanno and Hildebrandt, Andreas and Lenhof, Hans-Peter and Wesse, Tanja and Franke, Andre and Meese, Eckart and Keller, Andreas},
  journal   = {Oncotarget},
  title     = {{I}ntegrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: {A} lung cancer showcase},
  year      = {2016},
  number    = {12},
  pages     = {14857--14870},
  volume    = {7},
  doi       = {10.18632/oncotarget.7562},
}

@Article{WTG+18,
  author    = {Holly M. Wobma and Manuel A. Tamargo and Shahar Goeta and Lewis M. Brown and Raimon Duran-Struuck and Gordana Vunjak-Novakovic},
  journal   = {Biomaterials},
  title     = {{T}he influence of hypoxia and {IFN}-$\gamma$ on the proteome and metabolome of therapeutic mesenchymal stem cells},
  year      = {2018},
  pages     = {226--234},
  volume    = {167},
  doi       = {10.1016/j.biomaterials.2018.03.027},
}

@Article{PDT+19,
  author    = {Park, Jung Eun and Dutta, Bamaprasad and Tse, Shun Wilford and Gupta, Nikhil and Tan, Chee Fan and Low, Jee Keem and Yeoh, Kheng Wei and Kon, Oi Lian and Tam, James P. and Sze, Siu Kwan},
  journal   = {Oncogene},
  title     = {{H}ypoxia-induced tumor exosomes promote {M}2-like macrophage polarization of infiltrating myeloid cells and micro{RNA}-mediated metabolic shift},
  year      = {2019},
  pages     = {5158--5173},
  volume    = {38},
  doi       = {10.1038/s41388-019-0782-x},
}

@Article{NJVS19,
  author    = {Najgebauer, Hanna and Jarnuczak, Andrew F. and Varro, Andrea and Sanderson, Christopher M.},
  journal   = {Cancers},
  title     = {{I}ntegrative omic profiling reveals unique hypoxia induced signatures in gastric cancer associated myofibroblasts},
  year      = {2019},
  number    = {2},
  pages     = {263},
  volume    = {11},
  doi       = {10.3390/cancers11020263},
}

@Article{CLY+18,
  author    = {Chen, Jeng-Ting and Liu, Chien-Chun and Yu, Jau-Song and Li, Hung-Hsuan and Lai, Ming-Chih},
  journal   = {Journal of Proteomics},
  title     = {{I}ntegrated omics profiling identifies hypoxia-regulated genes in {HCT}116 colon cancer cells},
  year      = {2018},
  pages     = {139--151},
  volume    = {188},
  doi       = {10.1016/j.jprot.2018.02.031},
}

@Article{ZXS+17,
  author    = {Zhang, Kangling and Xu, Pei and Sowers, James L. and Machuca, Daniel F. and Mirfattah, Barsam and Herring, Jason and Tang, Hui and Chen, Yan and Tian, Bing and Brasier, Allan R. and Sowers, Lawrence C.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{P}roteome analysis of hypoxic glioblastoma cells reveals sequential metabolic adaptation of one-carbon metabolic pathways},
  year      = {2017},
  number    = {11},
  pages     = {1906--1921},
  volume    = {16},
  doi       = {10.1074/mcp.RA117.000154},
}

@Article{CGH+17,
  author    = {Cosme, Jake and Guo, Hongbo and Hadipour-Lakmehsari, Sina and Emili, Andrew and Gramolini, Anthony O.},
  journal   = {Journal of Proteome Research},
  title     = {{H}ypoxia-induced changes in the fibroblast secretome, exosome, and whole-cell proteome using cultured, cardiac-derived cells isolated from neonatal mice},
  year      = {2017},
  number    = {8},
  pages     = {2836--2847},
  volume    = {16},
  doi       = {10.1021/acs.jproteome.7b00144},
}

@Article{SRS+13a,
  author    = {Salomon, Carlos and Ryan, Jennifer and Sobrevia, Luis and Kobayashi, Miharu and Ashman, Keith and Mitchell, Murray and Rice, Gregory E.},
  journal   = {PLOS One},
  title     = {{E}xosomal signaling during hypoxia mediates microvascular endothelial cell migration and vasculogenesis},
  year      = {2013},
  number    = {7},
  pages     = {e68451},
  volume    = {8},
  doi       = {10.1371/journal.pone.0068451},
}

@Article{CRS+15,
  author    = {Cox, Thomas R. and Rumney, Robin M. H. and Schoof, Erwin M. and Perryman, Lara and Høye, Anette M. and Agrawal, Ankita and Bird, Demelza and Latif, Norain Ab and Forrest, Hamish and Evans, Holly R. and Huggins, Iain D. and Lang, Georgina and Linding, Rune and Gartland, Alison and Erler, Janine T.},
  journal   = {Nature},
  title     = {{T}he hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase},
  year      = {2015},
  pages     = {106--110},
  volume    = {522},
  doi       = {10.1038/nature14492},
}

@Article{CZD+14,
  author    = {Chen, Shuijiao and Zhang, Jie and Duan, Lunxi and Zhang, Yu and Li, Cui and Liu, Deliang and Ouyang, Chunhui and Lu, Fanggen and Liu, Xiaowei},
  journal   = {American Journal of Physiology-Gastrointestinal and Liver Physiology},
  title     = {{I}dentification of {H}n{RNP} {M} as a novel biomarker for colorectal carcinoma by quantitative proteomics},
  year      = {2014},
  number    = {5},
  pages     = {G394--G403},
  volume    = {306},
  doi       = {10.1152/ajpgi.00328.2013},
}

@Article{QMB+17,
  author    = {Quesada-Calvo, Florence and Massot, Charlotte and Bertrand, Virginie and Longuesp{\'e}e, R{\'e}mi and Bl{\'e}tard, No{\"e}lla and Somja, Joan and Mazzucchelli, Gabriel and Smargiasso, Nicolas and Baiwir, Dominique and De Pauw-Gillet, Marie-Claire and Delvenne, Philippe and Malaise, Michel and Coimbra Marques, Carla and Polus, Marc and De Pauw, Edwin and Meuwis, Marie-Alice and Louis, Edouard},
  journal   = {Clinical Proteomics},
  title     = {{OLFM}4, {KNG}1 and {S}ec24{C} identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages},
  year      = {2017},
  number    = {1},
  pages     = {9},
  volume    = {14},
  doi       = {10.1186/s12014-017-9143-3},
}

@Article{NKG+17,
  author    = {Tomohisa Nishio and Nobuya Kurabe and Naoko Goto-Inoue and Toshio Nakamura and Haruhiko Sugimura and Mitsutoshi Setou and Masato Maekawa},
  journal   = {Clinica Chimica Acta},
  title     = {{I}mmunohistochemical expression analysis of leucine-rich {PPR}-motif-containing protein ({LRPPRC}), a candidate colorectal cancer biomarker identified by shotgun proteomics using i{TRAQ}},
  year      = {2017},
  pages     = {276--282},
  volume    = {471},
  doi       = {10.1016/j.cca.2017.06.011},
}

@Article{ZLY+17,
  author    = {Zhang, Yanbin and Liu, Yue and Ye, Yingjiang and Shen, Danhua and Zhang, Hui and Huang, Hongyan and Li, Sha and Wang, Shan and Ren, Jun},
  journal   = {Journal of Cancer Research and Clinical Oncology},
  title     = {{Q}uantitative proteome analysis of colorectal cancer-related differential proteins},
  year      = {2017},
  number    = {2},
  pages     = {233--241},
  volume    = {143},
  doi       = {10.1007/s00432-016-2274-5},
}

@Article{BHB+15,
  author    = {Sylvia F. Boj and Chang-Il Hwang and Lindsey A. Baker and Iok In Christine Chio and Dannielle D. Engle and Vincenzo Corbo and Myrthe Jager and Mariano Ponz-Sarvise and Hervé Tiriac and Mona S. Spector and Ana Gracanin and Tobiloba Oni and Kenneth H. Yu and Ruben van Boxtel and Meritxell Huch and Keith D. Rivera and John P. Wilson and Michael E. Feigin and Daniel Öhlund and Abram Handly-Santana and Christine M. Ardito-Abraham and Michael Ludwig and Ela Elyada and Brinda Alagesan and Giulia Biffi and Georgi N. Yordanov and Bethany Delcuze and Brianna Creighton and Kevin Wright and Youngkyu Park and Folkert H.M. Morsink and I. Quintus Molenaar and Inne H. Borel Rinkes and Edwin Cuppen and Yuan Hao and Ying Jin and Isaac J. Nijman and Christine Iacobuzio-Donahue and Steven D. Leach and Darryl J. Pappin and Molly Hammell and David S. Klimstra and Olca Basturk and Ralph H. Hruban and George Johan Offerhaus and Robert G.J. Vries and Hans Clevers and David A. Tuveson},
  journal   = {Cell},
  title     = {{O}rganoid models of human and mouse ductal pancreatic cancer},
  year      = {2015},
  number    = {1},
  pages     = {324--338},
  volume    = {160},
  doi       = {10.1016/j.cell.2014.12.021},
}

@Article{BZQ+14,
  author    = {Britton, David and Zen, Yoh and Quaglia, Alberto and Selzer, Stefan and Mitra, Vikram and Lößner, Christopher and Jung, Stephan and Böhm, Gitte and Schmid, Peter and Prefot, Petra and Hoehle, Claudia and Koncarevic, Sasa and Gee, Julia and Nicholson, Robert and Ward, Malcolm and Castellano, Leandro and Stebbing, Justin and Zucht, Hans Dieter and Sarker, Debashis and Heaton, Nigel and Pike, Ian},
  journal   = {PLOS One},
  title     = {{Q}uantification of pancreatic cancer proteome and phosphorylome: {I}ndicates molecular events likely contributing to cancer and activity of drug targets},
  year      = {2014},
  number    = {3},
  pages     = {e90948},
  volume    = {9},
  doi       = {10.1371/journal.pone.0090948},
}

@Article{WLC+17,
  author    = {Wang, Ke and Li, Hao and Chen, Ruo and Zhang, Yang and Sun, Xiu-Xuan and Huang, Wan and Bian, Huijie and Chen, Zhi-Nan},
  journal   = {Oncotarget},
  title     = {{C}ombination of {CALR} and {PDIA}3 is a potential prognostic biomarker for non-small cell lung cancer},
  year      = {2017},
  number    = {57},
  pages     = {96945--96957},
  volume    = {8},
  doi       = {10.18632/oncotarget.18547},
}

@Article{ZZD+12,
  author    = {Zeng, Gu-Qing and Zhang, Pang-Fei and Deng, Xingming and Yu, Feng-Lei and Li, Cui and Xu, Yan and Yi, Hong and Li, Mao-Yu and Hu, Rong and Zuo, Jian-Hong and Li, Xin-Hui and Wan, Xun-Xun and Qu, Jia-Quan and He, Qiu-Yan and Li, Jian-Huang and Ye, Xu and Chen, Yu and Li, Jiao-Yang and Xiao, Zhi-Qiang},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{I}dentification of candidate biomarkers for early detection of human lung squamous cell cancer by quantitative proteomics},
  year      = {2012},
  number    = {6},
  pages     = {M111.013946},
  volume    = {11},
  doi       = {10.1074/mcp.M111.013946},
}

@Article{ZZY+13,
  author    = {Zhang, Peng-Fei and Zeng, Gu-Qing and Yi, Lun-Zhao and Liu, Jian-Ping and Wan, Xun-Xun and Qu, Jia-Quan and Li, Jian-Huang and Li, Cui and Tang, Can-E and Hu, Rong and Ye, Xu and Chen, Yu and Chen, Zhu-Chu and Xiao, Zhi-Qiang},
  journal   = {Oncology Reports},
  title     = {{I}dentification of integrin β1 as a prognostic biomarker for human lung adenocarcinoma using 2{D}-{LC}-{MS}/{MS} combined with i{TRAQ} technology},
  year      = {2013},
  number    = {1},
  pages     = {341--349},
  volume    = {30},
  doi       = {10.3892/or.2013.2477},
}

@Article{MZH+14,
  author    = {Mirus, Justin E. and Zhang, Yuzheng and Hollingsworth, Michael A. and Solan, Joell L. and Lampe, Paul D. and Hingorani, Sunil R.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{S}patiotemporal proteomic analyses during pancreas cancer progression identifies serine/threonine stress kinase 4 ({STK}4) as a novel candidate biomarker for early stage disease},
  year      = {2014},
  number    = {12},
  pages     = {3484--3496},
  volume    = {13},
  doi       = {10.1074/mcp.M113.036517},
}

@Article{GWS+17,
  author    = {Gao, Yanyan and Wang, Xinzheng and Sang, Zhihong and Li, Zongcheng and Liu, Feng and Mao, Jie and Yan, Dan and Zhao, Yongqiang and Wang, Hongli and Li, Ping and Ying, Xiaomin and Zhang, Xuemin and He, Kun and Wang, Hongxia},
  journal   = {Scientific Reports},
  title     = {Quantitative proteomics by {SWATH}-{MS} reveals sophisticated metabolic reprogramming in hepatocellular carcinoma tissues},
  year      = {2017},
  pages     = {45913},
  volume    = {7},
  doi       = {10.1038/srep45913},
}

@Article{TMS+17,
  author    = {Tu, Chengjian and Mojica, Wilfrido and Straubinger, Robert M. and Li, Jun and Shen, Shichen and Qu, Miao and Nie, Lei and Roberts, Rick and An, Bo and Qu, Jun},
  journal   = {Proteomics: Clinical Applications},
  title     = {{Q}uantitative proteomic profiling of paired cancerous and normal colon epithelial cells isolated freshly from colorectal cancer patients},
  year      = {2017},
  volume    = {11},
  number    = {5-6},
  pages     = {1600155},
  doi       = {10.1002/prca.201600155},
}

@Article{JSP+19,
  author    = {Jevti\'c, \v{Z}ivojin and Stoll, Britta and Pfeiffer, Friedhelm and Sharma, Kundan and Urlaub, Henning and Marchfelder, Anita and Lenz, Christof},
  journal   = {Proteomics},
  title     = {{T}he response of \emph{{H}aloferax volcanii} to salt and temperature stress: {A} proteome study by label-free mass spectrometry},
  year      = {2019},
  number    = {20},
  pages     = {1800491},
  volume    = {19},
  doi       = {10.1002/pmic.201800491},
}

@Article{KAK+17,
  author    = {Gurjeet Kaur and Syed Azmal Ali and Sudarshan Kumar and Ashok Kumar Mohanty and Pradip Behare},
  journal   = {Journal of Proteomics},
  title     = {{L}abel-free quantitative proteomic analysis of \emph{{L}actobacillus fermentum} {NCDC} 400 during bile salt exposure},
  year      = {2017},
  pages     = {36--45},
  volume    = {167},
  doi       = {10.1016/j.jprot.2017.08.008},
}

@Article{LJC+18,
  author    = {Taewon Lee and So Hyun Jun and Chi Won Choi and Seung Il Kim and Je Chul Lee and Ji Hyun Shin},
  journal   = {Microbial Pathogenesis},
  title     = {{S}alt stress affects global protein expression profiles of extracellular membrane-derived vesicles of \emph{{L}isteria monocytogenes}},
  year      = {2018},
  pages     = {272--279},
  volume    = {115},
  doi       = {10.1016/j.micpath.2017.12.071},
}

@Article{LLYL17,
  author    = {Jieting Lin and Hebin Liang and Junwei Yan and Lixin Luo},
  journal   = {Journal of Proteomics},
  title     = {{T}he molecular mechanism and post-transcriptional regulation characteristic of \emph{{T}etragenococcus halophilus} acclimation to osmotic stress revealed by quantitative proteomics},
  year      = {2017},
  pages     = {1--14},
  volume    = {168},
  doi       = {10.1016/j.jprot.2017.08.014},
}

@Article{LYS+17,
  author    = {Long-Xian Lv and Ren Yan and Hai-Yan Shi and Ding Shi and Dai-Qiong Fang and Hui-Yong Jiang and Wen-Rui Wu and Fei-Fei Guo and Xia-Wei Jiang and Si-Lan Gu and Yun-Bo Chen and Jian Yao and Lan-Juan Li},
  journal   = {Journal of Proteomics},
  title     = {{I}ntegrated transcriptomic and proteomic analysis of the bile stress response in probiotic \emph{{L}actobacillus salivarius} {LI}01},
  year      = {2017},
  pages     = {216--229},
  volume    = {150},
  doi       = {10.1016/j.jprot.2016.08.021},
}

@Article{GCS+19,
  author    = {Talita Helen Bombardelli Gomig and Iglenir João Cavalli and Ricardo Lehtonen Rodrigues de Souza and Aline Castro Rodrigues Lucena and Michel Batista and Kelly Cavalcanti Machado and Fabricio Klerynton Marchini and Fabio Albuquerque Marchi and Rubens Silveira Lima and Cícero de Andrade Urban and Luciane Regina Cavalli and Enilze Maria de Souza Fonseca Ribeiro},
  journal   = {Data in Brief},
  title     = {{H}igh-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data},
  year      = {2019},
  pages     = {104125},
  volume    = {25},
  doi       = {10.1016/j.dib.2019.104125},
}

@Article{SWW+18,
  author    = {Yang Song and Qing Wang and Desheng Wang and Junqiang Li and Jing Yang and Hong Li and Xiang Wang and Xuerong Jin and Ruirui Jing and Jing-Hua Yang and Haichuan Su},
  journal   = {Translational Oncology},
  title     = {{L}abel-free quantitative proteomics unravels carboxypeptidases as the novel biomarker in pancreatic ductal adenocarcinoma},
  year      = {2018},
  number    = {3},
  pages     = {691--699},
  volume    = {11},
  doi       = {10.1016/j.tranon.2018.03.005},
}

@Article{KJK+18,
  author    = {Kim, Young Eun and Jeon, Hyo Jin and Kim, Dahee and Lee, Sun Young and Kim, Ki Young and Hong, Jongki and Maeng, Pil Jae and Kim, Kwang-Rok and Kang, Dukjin},
  journal   = {Scientific Reports},
  title     = {{Q}uantitative proteomic analysis of 2{D} and 3{D} cultured colorectal cancer cells: {P}rofiling of tankyrase inhibitor {XAV}939-induced proteome},
  year      = {2018},
  number    = {1},
  pages     = {13255},
  volume    = {8},
  doi       = {10.1038/s41598-018-31564-6},
}

@Article{LKK+18,
  author    = {Lee, Janet and Kim, Hyun-Soo and Kim, Su-Min and Kim, Dong-Ik and Lee, Chang-Woo},
  journal   = {Molecules and Cells},
  title     = {{H}ypoxia upregulates mitotic cyclins which contribute to the multipotency of human mesenchymal stem cells by expanding proliferation lifespan},
  year      = {2018},
  number    = {3},
  pages     = {207--213},
  volume    = {41},
  doi       = {10.14348/molcells.2018.2231},
}

@Article{CSK+19,
  author    = {Chachami, Georgia and Stankovic-Valentin, Nicolas and Karagiota, Angeliki and Basagianni, Angeliki and Plessmann, Uwe and Urlaub, Henning and Melchior, Frauke and Simos, George},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{H}ypoxia-induced changes in {SUMO} conjugation affect transcriptional regulation under low oxygen},
  year      = {2019},
  number    = {6},
  pages     = {1197--1209},
  volume    = {18},
  doi       = {10.1074/mcp.RA119.001401},
}

@Article{JVC+12,
  author    = {{de Jong}, Olivier G. and Marianne C. Verhaar and Yong Chen and Pieter Vader and Hendrik Gremmels and George Posthuma and Raymond M. Schiffelers and Marjan Gucek and van Balkom, Bas W.M.},
  journal   = {Journal of Extracellular Vesicles},
  title     = {{C}ellular stress conditions are reflected in the protein and {RNA} content of endothelial cell-derived exosomes},
  year      = {2012},
  number    = {1},
  pages     = {18396},
  volume    = {1},
  doi       = {10.3402/jev.v1i0.18396},
}

@Article{ZAH+19,
  author    = {Qimin Zhou and Roland Andersson and Dingyuan Hu and Monika Bauden and Theresa Kristl and Agata Sasor and Krzysztof Pawłowski and Indira Pla and Katarzyna Said Hilmersson and Mengtao Zhou and Fan Lu and György Marko-Varga and Daniel Ansari},
  journal   = {EBioMedicine},
  title     = {{Q}uantitative proteomics identifies brain acid soluble protein 1 ({BASP}1) as a prognostic biomarker candidate in pancreatic cancer tissue},
  year      = {2019},
  pages     = {282--294},
  volume    = {43},
  doi       = {10.1016/j.ebiom.2019.04.008},
}

@Article{ZYW+19,
  author    = {Zhou, Bo and Yan, Yiwu and Wang, Yang and You, Sungyong and Freeman, Michael R. and Yang, Wei},
  journal   = {Clinical Proteomics},
  title     = {{Q}uantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer},
  year      = {2019},
  number    = {1},
  pages     = {15},
  volume    = {16},
  doi       = {10.1186/s12014-019-9236-2},
}

@Article{GTR+08,
  author    = {Garbis, Spiros D. and Tyritzis, Stavros I. and Roumeliotis, Theodoros and Zerefos, Panagiotis and Giannopoulou, Eugenia G. and Vlahou, Antonia and Kossida, Sophia and Diaz, Jose and Vourekas, Stavros and Tamvakopoulos, Constantin and Pavlakis, Kitty and Sanoudou, Despina and Constantinides, Constantinos A.},
  journal   = {Journal of Proteome Research},
  title     = {{S}earch for potential markers for prostate cancer diagnosis, prognosis and treatment in clinical tissue specimens using amine-specific isobaric tagging (i{TRAQ}) with two-dimensional liquid chromatography and tandem mass spectrometry},
  year      = {2008},
  number    = {8},
  pages     = {3146--3158},
  volume    = {7},
  doi       = {10.1021/pr800060r},
}

@Article{HZH+12,
  author    = {Han, Zhao-Dong and Zhang, Yan-Qiong and He, Hui-Chan and Dai, Qi-Shan and Qin, Guo-Qiang and Chen, Jia-Hong and Cai, Chao and Fu, Xin and Bi, Xue-Cheng and Zhu, Jian-Guo and Liao, Dong-Jiang and Lu, Xin-Peng and Mo, Zi-Yao and Zhu, Yun-Ping and Zhong, Wei-De},
  journal   = {Medical Oncology},
  title     = {{I}dentification of novel serological tumor markers for human prostate cancer using integrative transcriptome and proteome analysis},
  year      = {2012},
  number    = {4},
  pages     = {2877--2888},
  volume    = {29},
  doi       = {10.1007/s12032-011-0149-9},
}

@Article{JHZ+13,
  author    = {Jiang, Fu-Neng and He, Hui-Chan and Zhang, Yan-Qiong and Yang, Deng-Liang and Huang, Jie-Hong and Zhu, Yun-Xin and Mo, Ru-Jun and Chen, Guo and Yang, Sheng-Bang and Chen, Yan-Ru and Zhong, Wei-De and Zhou, Wen-Liang},
  journal   = {PLOS One},
  title     = {{A}n integrative proteomics and interaction network-based classifier for prostate cancer diagnosis},
  year      = {2013},
  number    = {5},
  pages     = {e63941},
  volume    = {8},
  doi       = {10.1371/journal.pone.0063941},
}

@Article{MMF+20,
  author    = {Mantsiou, Anna and Makridakis, Manousos and Fasoulakis, Konstantinos and Katafigiotis, Ioannis and Constantinides, Constantinos A. and Zoidakis, Jerome and Roubelakis, Maria G. and Vlahou, Antonia and Lygirou, Vasiliki},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteomics analysis of formalin fixed paraffin embedded tissues in the investigation of prostate cancer},
  year      = {2020},
  number    = {7},
  pages     = {2631--2642},
  volume    = {19},
  doi       = {10.1021/acs.jproteome.9b00587},
}

@Article{LPK+19,
  author    = {Lee, Sun Young and Park, Sung Bum and Kim, Young Eun and Yoo, Hee Min and Hong, Jongki and Choi, Kyoung-Jin and Kim, Ki Young and Kang, Dukjin},
  journal   = {Scientific Reports},
  title     = {{iTRAQ}-based quantitative proteomic comparison of 2{D} and 3{D} adipocyte cell models co-cultured with macrophages using online 2{D}-nano{LC}-{ESI}-{MS}/{MS}},
  year      = {2019},
  number    = {1},
  pages     = {16746},
  volume    = {9},
  doi       = {10.1038/s41598-019-53196-0},
}

@Article{RTA+15,
  author        = {Ramteke, Anand and Ting, Harold and Agarwal, Chapla and Mateen, Samiha and Somasagara, Ranganathan and Hussain, Anowar and Graner, Michael and Frederick, Barbara and Agarwal, Rajesh and Deep, Gagan},
  journal       = {Molecular Carcinogenesis},
  title         = {{E}xosomes secreted under hypoxia enhance invasiveness and stemness of prostate cancer cells by targeting adherens junction molecules},
  year          = {2015},
  volume        = {54},
  number        = {7},
  pages         = {554--565},
  doi           = {10.1002/mc.22124},
}

@Article{SKA+13,
  author    = {Salomon, Carlos and Kobayashi, Miharu and Ashman, Keith and Sobrevia, Luis and Mitchell, Murray D. and Rice, Gregory E.},
  journal   = {PLOS One},
  title     = {{H}ypoxia-induced changes in the bioactivity of cytotrophoblast-derived exosomes},
  year      = {2013},
  number    = {11},
  pages     = {e79636},
  volume    = {8},
  doi       = {10.1371/journal.pone.0079636},
}

@Article{HKX+14,
  author    = {He, Weiqi and Kuang, Yongqin and Xing, Xuemin and Simpson, Richard J. and Huang, Haidong and Yang, Tao and Chen, Jingmin and Yang, Libin and Liu, Enyu and He, Weifeng and Gu, Jianwen},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteomic comparison of 3{D} and 2{D} glioma models reveals increased {HLA}-{E} expression in 3{D} models is associated with resistance to {NK} cell-mediated cytotoxicity},
  year      = {2014},
  number    = {5},
  pages     = {2272--2281},
  volume    = {13},
  doi       = {10.1021/pr500064m},
}

@Article{HLC19,
  author    = {Tracey Hurrell and Kathryn S. Lilley and Allan Duncan Cromarty},
  journal   = {Toxicology Letters},
  title     = {{P}roteomic responses of {H}ep{G}2 cell monolayers and 3{D} spheroids to selected hepatotoxins},
  year      = {2019},
  pages     = {40--50},
  volume    = {300},
  doi       = {10.1016/j.toxlet.2018.10.030},
}

@Article{MTK+15,
  author    = {Musrap, Natasha and Tuccitto, Alessandra and Karagiannis, George S. and Saraon, Punit and Batruch, Ihor and Diamandis, Eleftherios P.},
  journal   = {Journal of Biological Chemistry},
  title     = {{C}omparative proteomics of ovarian cancer aggregate formation reveals an increased expression of calcium-activated chloride channel regulator 1 ({CLCA}1)},
  year      = {2015},
  number    = {28},
  pages     = {17218--17227},
  volume    = {290},
  doi       = {10.1074/jbc.m115.639773},
}

@Article{PLC+10,
  author    = {Pruksakorn, Dumnoensun and Lirdprapamongkol, Kriengsak and Chokchaichamnankit, Daranee and Subhasitanont, Pantipa and Chiablaem, Khajeelak and Svasti, Jisnuson and Srisomsap, Chantragan},
  journal   = {Proteomics},
  title     = {{M}etabolic alteration of {H}ep{G}2 in scaffold-based 3-{D} culture: {P}roteomic approach},
  year      = {2010},
  volume    = {10},
  number    = {21},
  pages     = {3896--3904},
  doi       = {10.1002/pmic.201000137},
}

@Article{YYW+13,
  author    = {Yan, Ming and Yang, Xihu and Wang, Lizhen and Clark, David and Zuo, Hui and Ye, Dongxia and Chen, Wantao and Zhang, Ping},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{P}lasma membrane proteomics of tumor spheres identify {CD}166 as a novel marker for cancer stem-like cells in head and neck squamous cell carcinoma},
  year      = {2013},
  number    = {11},
  pages     = {3271--3284},
  volume    = {12},
  doi       = {10.1074/mcp.M112.025460},
}

@Article{KRN+19,
  author    = {Kawahara, Rebeca and Recuero, Saulo and Nogueira, Fabio C. S. and Domont, Gilberto B. and Leite, Katia R. M. and Srougi, Miguel and Thaysen-Andersen, Morten and Palmisano, Giuseppe},
  journal   = {Proteomics},
  title     = {{T}issue proteome signatures associated with five grades of prostate cancer and benign prostatic hyperplasia},
  year      = {2019},
  volume    = {19},
  number    = {21-22},
  pages     = {1900174},
  doi       = {10.1002/pmic.201900174},
}

@Article{AKG+18,
  author    = {Atak, Apurva and Khurana, Samiksha and Gollapalli, Kishore and Reddy, Panga Jaipal and Levy, Roei and Ben-Salmon, Stav and Hollander, Dror and Donyo, Maya and Heit, Anke and Hotz-Wagenblatt, Agnes and Biran, Hadas and Sharan, Roded and Rane, Shailendra and Shelar, Ashutosh and Ast, Gil and Srivastava, Sanjeeva},
  journal   = {Oncotarget},
  title     = {{Q}uantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas},
  year      = {2018},
  number    = {17},
  pages     = {13530--13544},
  volume    = {9},
  doi       = {10.18632/oncotarget.24418},
}

@Article{GLZ+18,
  author    = {Guo, Tiannan and Li, Li and Zhong, Qing and Rupp, Niels J and Charmpi, Konstantina and Wong, Christine E and Wagner, Ulrich and Rueschoff, Jan H and Jochum, Wolfram and Fankhauser, Christian Daniel and Saba, Karim and Poyet, Cedric and Wild, Peter J and Aebersold, Ruedi and Beyer, Andreas},
  journal   = {Life Science Alliance},
  title     = {{M}ulti-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers},
  year      = {2018},
  number    = {2},
  pages     = {e201800042},
  volume    = {1},
  doi       = {10.26508/lsa.201800042},
}

@Article{HZW+17,
  author    = {Hao, Jian-Jiang and Zhi, Xiaofei and Wang, Yeming and Zhang, Zheng and Hao, Zeyu and Ye, Rong and Tang, Zhijie and Qian, Fei and Wang, Quhui and Zhu, Jianwei},
  journal   = {Scientific Reports},
  title     = {{C}omprehensive proteomic characterization of the human colorectal carcinoma reveals signature proteins and perturbed pathways},
  year      = {2017},
  number    = {1},
  pages     = {42436},
  volume    = {7},
  doi       = {10.1038/srep42436},
}

@Article{CHO+18,
  author    = {Coleman, Orla and Henry, Michael and O'Neill, Fiona and Roche, Sandra and Swan, Niall and Boyle, Lorraine and Murphy, Jean and Meiller, Justine and Conlon, Neil T. and Geoghegan, Justin and Conlon, Kevin C. and Lynch, Vincent and Straubinger, Ninfa L. and Straubinger, Robert M. and McVey, Gerard and Moriarty, Michael and Meleady, Paula and Clynes, Martin},
  journal   = {Proteomes},
  title     = {{A} comparative quantitative {LC}-{MS}/{MS} profiling analysis of human pancreatic adenocarcinoma, adjacent-normal tissue, and patient-derived tumour xenografts},
  year      = {2018},
  number    = {4},
  pages     = {45},
  volume    = {6},
  doi       = {10.3390/proteomes6040045},
}

@Article{FPR+18,
  author    = {Francesca Felice and Anna Maria Piras and Silvia Rocchiccioli and Maria Chiara Barsotti and Tatiana Santoni and Angela Pucci and Silvia Burchielli and Federica Chiellini and Nadia Ucciferri and Roberto Solaro and Angelina Altomare and Antonella Cecchettini and Rossella Di Stefano},
  journal   = {International Journal of Pharmaceutics},
  title     = {{E}ndothelial progenitor cell secretome delivered by novel polymeric nanoparticles in ischemic hindlimb},
  year      = {2018},
  number    = {1},
  pages     = {82--89},
  volume    = {542},
  doi       = {10.1016/j.ijpharm.2018.03.015},
}

@Article{ODS+18,
  author    = {Ontoria-Oviedo, Imelda and Dorronsoro, Akaitz and Sánchez, Rafael and Ciria, Maria and Gómez-Ferrer, Marta and Buigues, Marc and Grueso, Elena and Tejedor, Sandra and García-García, Francisco and González-King, Hernán and Garcia, Nahuel A. and Peiró-Molina, Esteban and Sepúlveda, Pilar},
  journal   = {Frontiers in Cardiovascular Medicine},
  title     = {{E}xtracellular vesicles secreted by hypoxic {AC}10 cardiomyocytes modulate fibroblast cell motility},
  year      = {2018},
  pages     = {152},
  volume    = {5},
  doi       = {10.3389/fcvm.2018.00152},
}

@Article{KAN+19,
  author    = {Kugeratski, Fernanda G. and Atkinson, Samuel J. and Neilson, Lisa J. and Lilla, Sergio and Knight, John R. P. and Serneels, Jens and Juin, Amelie and Ismail, Shehab and Bryant, David M. and Markert, Elke K. and Machesky, Laura M. and Mazzone, Massimiliano and Sansom, Owen J. and Zanivan, Sara},
  journal   = {Science Signaling},
  title     = {{H}ypoxic cancer-associated fibroblasts increase {NCBP}2-{AS}2/{HIAR} to promote endothelial sprouting through enhanced {VEGF} signaling},
  year      = {2019},
  number    = {567},
  pages     = {eaan8247},
  volume    = {12},
  doi       = {10.1126/scisignal.aan8247},
}

@Article{JSZ+19,
  author    = {Jiang, Ying and Sun, Aihua and Zhao, Yang and Ying, Wantao and Sun, Huichuan and Yang, Xinrong and Xing, Baocai and Sun, Wei and Ren, Liangliang and Hu, Bo and Li, Chaoying and Zhang, Li and Qin, Guangrong and Zhang, Menghuan and Chen, Ning and Zhang, Manli and Huang, Yin and Zhou, Jinan and Zhao, Yan and Liu, Mingwei and Zhu, Xiaodong and Qiu, Yang and Sun, Yanjun and Huang, Cheng and Yan, Meng and Wang, Mingchao and Liu, Wei and Tian, Fang and Xu, Huali and Zhou, Jian and Wu, Zhenyu and Shi, Tieliu and Zhu, Weimin and Qin, Jun and Xie, Lu and Fan, Jia and Qian, Xiaohong and He, Fuchu and He, Fuchu and Qian, Xiaohong and Qin, Jun and Jiang, Ying and Ying, Wantao and Sun, Wei and Zhu, Yunping and Zhu, Weimin and Wang, Yi and Yang, Dong and Liu, Wanlin and Liu, Qiongming and Yang, Xiaoming and Zhen, Bei and Wu, Zhenyu and Fan, Jia and Sun, Huichuan and Qian, Juying and Hong, Tao and Shen, Lin and Xing, Baocai and Yang, Pengyuan and Shen, Huali and Zhang, Lijuan and Cheng, Shujun and Cai, Jianqiang and Zhao, Xiaohang and Sun, Yulin and Xiao, Ting and Mao, Yousheng and Chen, Xiangmei and Wu, Di and Chen, Lin and Dong, Jun and Deng, Haiteng and Tan, Minjia and Wu, Zhixing and Zhao, Qingchuan and Shen, Zhongyang and Chen, Xinguo and Gao, Youhe and Sun, Wei and Wang, Tong and Liu, Siqi and Lin, Liang and Zi, Jin and Lou, Xiaomin and Zeng, Rong and Wu, Yi and Cai, Sanjun and Jiang, Bo and Chen, Anqing and Li, Zijian and Yang, Fuquan and Chen, Xiulan and Sun, Yuna and Wang, Quanli and Zhang, Yi and Wang, Guangshun and Chen, Zhuchu and Qin, Weisong and Li, Zesong and {Chinese Human Proteome Project Consortium (CNHPP)}},
  journal   = {Nature},
  title     = {Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma},
  year      = {2019},
  number    = {7747},
  pages     = {257--261},
  volume    = {567},
  doi       = {10.1038/s41586-019-0987-8},
}

@Article{LZW+17,
  author    = {Li, Wei and Zhang, Xuede and Wang, Wei and Sun, Ruiying and Liu, Boxuan and Ma, Yuefeng and Zhang, Wei and Ma, Li and Jin, Yaofeng and Yang, Shuanying},
  journal   = {American Journal of Translational Research},
  title     = {{Q}uantitative proteomics analysis of mitochondrial proteins in lung adenocarcinomas and normal lung tissue using i{TRAQ} and tandem mass spectrometry},
  year      = {2017},
  number    = {9},
  pages     = {3918--3934},
  volume    = {9},
  url       = {https://www.ncbi.nlm.nih.gov/pubmed/28979670},
}

@Article{BLL+16,
  author    = {Backes, Christina and Ludwig, Nicole and Leidinger, Petra and Huwer, Hanno and Tenzer, Stefan and Fehlmann, Tobias and Franke, Andre and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
  journal   = {Oncotarget},
  title     = {{P}aired proteomics, transcriptomics and mi{RN}omics in non-small cell lung cancers: {K}nown and novel signaling cascades},
  year      = {2016},
  number    = {44},
  pages     = {71514--71525},
  volume    = {7},
  doi       = {10.18632/oncotarget.11723},
}

@Article{LLL+17,
  author    = {Li, Guoqing and Li, Maoyu and Liang, Xujun and Xiao, Zhefeng and Zhang, Pengfei and Shao, Meiying and Peng, Fang and Chen, Yongheng and Li, Yuanyuan and Chen, Zhuchu},
  journal   = {Journal of Cancer},
  title     = {{I}dentifying {DCN} and {HSPD}1 as potential biomarkers in colon cancer using 2{D}-{LC}-{MS}/{MS} combined with i{TRAQ} technology},
  year      = {2017},
  number    = {3},
  pages     = {479--489},
  volume    = {8},
  doi       = {10.7150/jca.17192},
}

@Article{WYL+19,
  author    = {Wang, Guoqiang and Yang, Qiongzhi and Li, Maoyu and Zhang, Ye and Cai, Yuxiang and Liang, Xujun and Fu, Ying and Xiao, Zhefeng and Zhou, Minze and Xie, Zhongpeng and Huang, Huichao and Huang, Yahui and Chen, Yongheng and He, Qiongqiong and Peng, Fang and Chen, Zhuchu},
  journal   = {Biology Open},
  title     = {{Q}uantitative proteomic profiling of tumor-associated vascular endothelial cells in colorectal cancer},
  year      = {2019},
  number    = {5},
  pages     = {bio042838},
  volume    = {8},
  doi       = {10.1242/bio.042838},
}

@Article{KNT+15,
  author    = {Kato, Yasufumi and Nakamura, Haruhiko and Tojo, Hiromasa and Nomura, Masaharu and Nagao, Toshitaka and Kawamura, Takeshi and Kodama, Tatsuhiko and Ohira, Tatsuo and Ikeda, Norihiko and Fehniger, Thomas and Marko-Varga, György and Nishimura, Toshihide and Kato, Harubumi},
  journal   = {Clinical and Translational Medicine},
  title     = {{A} proteomic profiling of laser-microdissected lung adenocarcinoma cells of early lepidic-types},
  year      = {2015},
  number    = {1},
  pages     = {24},
  volume    = {4},
  doi       = {10.1186/s40169-015-0064-3},
}

@Article{ZLS+14,
  author    = {Zhuo, Huiqin and Lyu, Zhi and Su, Jing and He, Jian and Pei, Yihua and Cheng, Xiao and Zhou, Nuo and Lu, Xiaoling and Zhou, Sufang and Zhao, Yongxiang},
  journal   = {Journal of Proteome Research},
  title     = {{E}ffect of lung squamous cell carcinoma tumor microenvironment on the {CD}105+ endothelial cell proteome},
  year      = {2014},
  number    = {11},
  pages     = {4717--4729},
  volume    = {13},
  doi       = {10.1021/pr5006229},
}

@Article{GADS19,
  author    = {Gęgotek, Agnieszka and Atalay, Sinemyiz and Domingues, Pedro and Skrzydlewska, Elżbieta},
  journal   = {Cells},
  title     = {{T}he differences in the proteome profile of cannabidiol-treated skin fibroblasts following {UVA} or {UVB} irradiation in 2{D} and 3{D} cell cultures},
  year      = {2019},
  number    = {9},
  pages     = {995},
  volume    = {8},
  doi       = {10.3390/cells8090995},
}

@Article{ZZL+19,
  author    = {Zhu, Yi and Zhu, Jiang and Lu, Cong and Zhang, Qiushi and Xie, Wei and Sun, Ping and Dong, Xiaochuan and Yue, Liang and Sun, Yaoting and Yi, Xiao and Zhu, Tiansheng and Ruan, Guan and Aebersold, Ruedi and Huang, Shi'ang and Guo, Tiannan},
  journal   = {Proteomics: Clinical Applications},
  title     = {{I}dentification of protein abundance changes in hepatocellular carcinoma tissues using {PCT}–{SWATH}},
  year      = {2019},
  number    = {1},
  pages     = {1700179},
  volume    = {13},
  doi       = {10.1002/prca.201700179},
}

@Article{BOK+18,
  author    = {Buczak, Katarzyna and Ori, Alessandro and Kirkpatrick, Joanna M. and Holzer, Kerstin and Dauch, Daniel and Roessler, Stephanie and Endris, Volker and Lasitschka, Felix and Parca, Luca and Schmidt, Alexander and Zender, Lars and Schirmacher, Peter and Krijgsveld, Jeroen and Singer, Stephan and Beck, Martin},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {Spatial tissue proteomics quantifies inter- and intratumor heterogeneity in hepatocellular carcinoma ({HCC})},
  year      = {2018},
  number    = {4},
  pages     = {810--825},
  volume    = {17},
  doi       = {10.1074/mcp.RA117.000189},
}

@Article{ZMH+13,
  author    = {Zanivan, Sara and Maione, Federica and Hein, Marco Y. and Hern{\'a}ndez-Fernaud, Juan Ramon and Ostasiewicz, Pawel and Giraudo, Enrico and Mann, Matthias},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {{SILAC}-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers},
  year      = {2013},
  number    = {12},
  pages     = {3599--3611},
  volume    = {12},
  doi       = {10.1074/mcp.M113.031344},
}

@Article{STA+19,
  author    = {Saleem, Saira and Tariq, Sahrish and Aleem, Iffat and Sadr-ul Shaheed and Tahseen, Muhammad and Atiq, Aribah and Hassan, Sadia and Abu Bakar, Muhammad and Khattak, Shahid and Syed, Aamir Ali and Ahmad, Asad Hayat and Hussain, Mudassar and Yusuf, Muhammed Aasim and Sutton, Chris},
  journal   = {Clinical Proteomics},
  title     = {{P}roteomics analysis of colon cancer progression},
  year      = {2019},
  number    = {1},
  pages     = {44},
  volume    = {16},
  doi       = {10.1186/s12014-019-9264-y},
}

@Article{BCMS20,
  author    = {Bush, Jacob T. and Chan, Mun Chiang and Mohammed, Shabaz and Schofield, Christopher},
  journal   = {ChemBioChem},
  title     = {{Q}uantitative {MS}-based proteomics comparing the {MCF}-7 cellular response to hypoxia and a 2-oxoglutarate analogue},
  year      = {2020},
  number    = {11},
  pages     = {1647--1655},
  volume    = {21},
  doi       = {10.1002/cbic.201900719},
}

@Article{RVN+20,
  author    = {Ross, James A. and Vissers, Johannes P.C. and Nanda, Jyoti and Stewart, Grant D. and Husi, Holger and Habib, Fouad K. and Hammond, Dean E. and Gethings, Lee A.},
  journal   = {Clinical Chemistry and Laboratory Medicine},
  title     = {{T}he influence of hypoxia on the prostate cancer proteome},
  year      = {2020},
  number    = {6},
  pages     = {980--993},
  volume    = {58},
  doi       = {10.1515/cclm-2019-0626},
}

@Article{LPK+13,
  author    = {Lee, Ji Yoon and Pajarillo, Edward Alain B. and Kim, Min Jeong and Chae, Jong Pyo and Kang, Dae-Kyung},
  journal   = {Journal of Proteome Research},
  title     = {{P}roteomic and transcriptional analysis of \emph{{L}actobacillus johnsonii} {PF01} during bile salt exposure by {iTRAQ} shotgun proteomics and quantitative {RT-PCR}},
  year      = {2013},
  number    = {1},
  pages     = {432--443},
  volume    = {12},
  doi       = {10.1021/pr300794y},
}

@Article{MGF+19,
  author    = {Ming, Tinghong and Geng, Lingxin and Feng, Ying and Lu, Chenyang and Zhou, Jun and Li, Yanyan and Zhang, Dijun and He, Shan and Li, Ye and Cheong, Lingzhi and Su, Xiurong},
  journal   = {Frontiers in Microbiology},
  title     = {{iTRAQ}-based quantitative proteomic profiling of \emph{{S}taphylococcus aureus} under different osmotic stress conditions},
  year      = {2019},
  pages     = {1082},
  volume    = {10},
  doi       = {10.3389/fmicb.2019.01082},
}

@Article{VHW+19,
  author    = {Suhas Vasaikar and Chen Huang and Xiaojing Wang and Vladislav A. Petyuk and Sara R. Savage and Bo Wen and Yongchao Dou and Yun Zhang and Zhiao Shi and Osama A. Arshad and Marina A. Gritsenko and Lisa J. Zimmerman and Jason E. McDermott and Therese R. Clauss and Ronald J. Moore and Rui Zhao and Matthew E. Monroe and Yi-Ting Wang and Matthew C. Chambers and Robbert J.C. Slebos and Ken S. Lau and Qianxing Mo and Li Ding and Matthew Ellis and Mathangi Thiagarajan and Christopher R. Kinsinger and Henry Rodriguez and Richard D. Smith and Karin D. Rodland and Daniel C. Liebler and Tao Liu and Bing Zhang and Akhilesh Pandey and Amanda Paulovich and Andrew Hoofnagle and D.R. Mani and Daniel W. Chan and David F. Ransohoff and David Fenyo and David L. Tabb and Douglas A. Levine and Emily S. Boja and Eric Kuhn and Forest M. White and Gordon A. Whiteley and Heng Zhu and Hui Zhang and Ie-Ming Shih and Jasmin Bavarva and Jeffrey Whiteaker and Karen A. Ketchum and Karl R. Clauser and Kelly Ruggles and Kimberly Elburn and Linda Hannick and Mark Watson and Mauricio Oberti and Mehdi Mesri and Melinda E. Sanders and Melissa Borucki and Michael A. Gillette and Michael Snyder and Nathan J. Edwards and Negin Vatanian and Paul A. Rudnick and Peter B. McGarvey and Philip Mertins and R. Reid Townsend and Ratna R. Thangudu and Robert C. Rivers and Samuel H. Payne and Sherri R. Davies and Shuang Cai and Stephen E. Stein and Steven A. Carr and Steven J. Skates and Subha Madhavan and Tara Hiltke and Xian Chen and Yingming Zhao and Yue Wang and Zhen Zhang},
  journal   = {Cell},
  title     = {Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities},
  year      = {2019},
  number    = {4},
  pages     = {1035--1049},
  volume    = {177},
  doi       = {10.1016/j.cell.2019.03.030},
}

@Article{SHC+20,
  author    = {Sun, Rui and Hunter, Christie and Chen, Chen and Ge, Weigang and Morrice, Nick and Liang, Shuang and Zhu, Tiansheng and Yuan, Chunhui and Ruan, Guan and Zhang, Qiushi and Cai, Xue and Yu, Xiaoyan and Chen, Lirong and Dai, Shaozheng and Luan, Zhongzhi and Aebersold, Ruedi and Zhu, Yi and Guo, Tiannan},
  journal   = {Journal of Proteome Research},
  title     = {Accelerated protein biomarker discovery from {FFPE} tissue samples using single-shot, short gradient microflow {SWATH} {MS}},
  year      = {2020},
  number    = {7},
  pages     = {2732--2741},
  volume    = {19},
  doi       = {10.1021/acs.jproteome.9b00671},
}

@Article{GZD+19,
  author    = {Qiang Gao and Hongwen Zhu and Liangqing Dong and Weiwei Shi and Ran Chen and Zhijian Song and Chen Huang and Junqiang Li and Xiaowei Dong and Yanting Zhou and Qian Liu and Lijie Ma and Xiaoying Wang and Jian Zhou and Yansheng Liu and Emily Boja and Ana I. Robles and Weiping Ma and Pei Wang and Yize Li and Li Ding and Bo Wen and Bing Zhang and Henry Rodriguez and Daming Gao and Hu Zhou and Jia Fan},
  journal   = {Cell},
  title     = {Integrated proteogenomic characterization of HBV-related hepatocellular carcinoma},
  year      = {2019},
  number    = {2},
  pages     = {561--577},
  volume    = {179},
  doi       = {10.1016/j.cell.2019.08.052},
}

@Article{BLP+05,
  author    = {Blanc, Jean-Frédéric and Lalanne, Céline and Plomion, Christophe and Schmitter, Jean-Marie and Bathany, Katell and Gion, Jean-Marc and Bioulac-Sage, Paulette and Balabaud, Charles and Bonneu, Marc and Rosenbaum, Jean},
  journal   = {Proteomics},
  title     = {Proteomic analysis of differentially expressed proteins in hepatocellular carcinoma developed in patients with chronic viral hepatitis {C}},
  year      = {2005},
  number    = {14},
  pages     = {3778--3789},
  volume    = {5},
  doi       = {10.1002/pmic.200401194},
}

@Article{LTZ+05,
  author    = {Li, Chen and Tan, Ye-Xiong and Zhou, Hu and Ding, Shi-Jian and Li, Su-Jun and Ma, Dan-jun and Man, Xiao-bo and Hong, Yi and Zhang, Lei and Li, Long and Xia, Qi-Chang and Wu, Jia-Rui and Wang, Hong-Yang and Zeng, Rong},
  journal   = {Proteomics},
  title     = {Proteomic analysis of hepatitis {B} virus-associated hepatocellular carcinoma: {I}dentification of potential tumor markers},
  year      = {2005},
  number    = {4},
  pages     = {1125--1139},
  volume    = {5},
  doi       = {10.1002/pmic.200401141},
}

@Article{QPP+17,
  author    = {Zhiwei Qiao and Xiaoqing Pan and Cuneyd Parlayan and Hidenori Ojima and Tadashi Kondo},
  journal   = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
  title     = {Proteomic study of hepatocellular carcinoma using a novel modified aptamer-based array ({SOMAscan™}) platform},
  year      = {2017},
  number    = {4},
  pages     = {434--443},
  volume    = {1865},
  doi       = {10.1016/j.bbapap.2016.09.011},
}

@Article{GJZ+17,
  author    = {Guo, Jiao and Jing, Rui and Zhong, Jian-Hong and Dong, Xin and Li, Yun-Xi and Liu, Yin-Kun and Huang, Tian-Ren and Zhang, Chun-Yan},
  journal   = {Oncotarget},
  title     = {Identification of {CD14} as a potential biomarker of hepatocellular carcinoma using {iTRAQ} quantitative proteomics},
  year      = {2017},
  number    = {37},
  pages     = {62011--62028},
  volume    = {8},
  doi       = {10.18632/oncotarget.18782},
}

@Article{QXC+16,
  author    = {Qi, Yingzi and Xu, Feng and Chen, Lingsheng and Li, Yanchang and Xu, Zhongwei and Zhang, Yao and Wei, Wei and Su, Na and Zhang, Tao and Fan, Fengxu and Wang, Xing and Qin, Xue and Zhang, Lingqiang and Liu, Yinkun and Xu, Ping},
  journal   = {Oncotarget},
  title     = {Quantitative proteomics reveals {FLNC} as a potential progression marker for the development of hepatocellular carcinoma},
  year      = {2016},
  number    = {42},
  pages     = {68242--68252},
  volume    = {7},
  doi       = {10.18632/oncotarget.11921},
}

@Article{KHN+20,
  author    = {Kwon, Oh Kwang and Ha, Yun-Sok and Na, Ann-Yae and Chun, So Young and Kwon, Tae Gyun and Lee, Jun Nyung and Lee, Sangkyu},
  journal   = {Cancer Genomics - Proteomics},
  title     = {Identification of novel prognosis and prediction markers in advanced prostate cancer tissues based on quantitative proteomics},
  year      = {2020},
  number    = {2},
  pages     = {195--208},
  volume    = {17},
  doi       = {10.21873/cgp.20180},
}

@Article{BEM+20,
  author    = {Berndt, Nikolaus and Egners, Antje and Mastrobuoni, Guido and Vvedenskaya, Olga and Fragoulis, Athanassios and Dugourd, Aurélien and Bulik, Sascha and Pietzke, Matthias and Bielow, Chris and {van Gassel}, Rob and Damink, Steven W. Olde and Erdem, Merve and Saez-Rodriguez, Julio and Holzhütter, Hermann-Georg and Kempa, Stefan and Cramer, Thorsten},
  journal   = {British Journal of Cancer},
  title     = {Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer},
  year      = {2020},
  number    = {2},
  pages     = {233--244},
  volume    = {122},
  doi       = {10.1038/s41416-019-0659-3},
}

@Article{SPJ+20,
  author    = {Song, Zifeng and Pearce, Martin C. and Jiang, Yuan and Yang, Liping and Goodall, Cheri and Miranda, Cristobal L. and Milovancev, Milan and Bracha, Shay and Kolluri, Siva K. and Maier, Claudia S.},
  journal   = {Scientific Reports},
  title     = {Delineation of hypoxia-induced proteome shifts in osteosarcoma cells with different metastatic propensities},
  year      = {2020},
  number    = {1},
  pages     = {727},
  volume    = {10},
  doi       = {10.1038/s41598-019-56878-x},
}

@Article{GPT+19,
  author    = {Gupta, Nikhil and Park, Jung Eun and Tse, Wilford and Low, Jee Keem and Kon, Oi Lian and McCarthy, Neil and Sze, Siu Kwan},
  journal   = {Oncotarget},
  title     = {{ERO1α} promotes hypoxic tumor progression and is associated with poor prognosis in pancreatic cancer},
  year      = {2019},
  number    = {57},
  pages     = {5970--5982},
  volume    = {10},
  doi       = {10.18632/oncotarget.27235},
}

@Article{CWG+19,
  author    = {Chandran, Vineesh Indira and Welinder, Charlotte and Gonçalves de Oliveira, Kelin and Cerezo-Magaña, Myriam and Månsson, Ann-Sofie and Johansson, Maria C. and Marko-Varga, Gyorgy and Belting, Mattias},
  journal   = {Journal of Neuro-Oncology},
  title     = {Global extracellular vesicle proteomic signature defines {U87-MG} glioma cell hypoxic status with potential implications for non-invasive diagnostics},
  year      = {2019},
  number    = {3},
  pages     = {477--488},
  volume    = {144},
  doi       = {10.1007/s11060-019-03262-4},
}

@Article{JBG+18,
  author    = {Jacobsen, Mette D. and Beynon, Robert J. and Gethings, Lee A. and Claydon, Amy J. and Langridge, James I. and Vissers, Johannes P. C. and Brown, Alistair J. P. and Hammond, Dean E.},
  journal   = {Scientific Reports},
  title     = {Specificity of the osmotic stress response in \emph{{C}andida albicans} highlighted by quantitative proteomics},
  year      = {2018},
  number    = {1},
  pages     = {14492},
  volume    = {8},
  doi       = {10.1038/s41598-018-32792-6},
}

@Article{LLL+19,
  author    = {Li, Qiwen and Luo, Tao and Lu, Wenxin and Yi, Xiaoxiao and Zhao, Zhihe and Liu, Jun},
  journal   = {Proteome Science},
  title     = {Proteomic analysis of human periodontal ligament cells under hypoxia},
  year      = {2019},
  number    = {1},
  pages     = {3},
  volume    = {17},
  doi       = {10.1186/s12953-019-0151-2},
}

@Article{EWK+19,
  author    = {Friedrich Erhart and Tamara Weiss and Simone Klingenbrunner and Katrin Fischhuber and René Reitermaier and Angela Halfmann and Bernadette Blauensteiner and Daniela Lötsch and Sabine Spiegl-Kreinecker and Walter Berger and Fernando J. Sialana and Gert Lubec and Thomas Felzmann and Alexander Dohnal and Carmen Visus},
  journal   = {Cytotherapy},
  title     = {Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production},
  year      = {2019},
  number    = {6},
  pages     = {643--658},
  volume    = {21},
  doi       = {10.1016/j.jcyt.2019.03.002},
}

@Article{KDS+14,
  author    = {Konze, Sarah A. and van Diepen, Laura and Schr{\"o}der, Anke and Olmer, Ruth and M{\"o}ller, Hanna and Pich, Andreas and Wei{\ss}mann, Robert and Kuss, Andreas W. and Zweigerdt, Robert and Buettner, Falk F. R.},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {Cleavage of {E}-cadherin and β-catenin by calpain affects {W}nt signaling and spheroid formation in suspension cultures of human pluripotent stem cells},
  year      = {2014},
  number    = {4},
  pages     = {990--1007},
  volume    = {13},
  doi       = {10.1074/mcp.M113.033423},
}

@Article{KSK+18,
  author    = {Himel N. Khaleque and Raihan Shafique and Anna H. Kaksonen and Naomi J. Boxall and Elizabeth L.J. Watkin},
  journal   = {Research in Microbiology},
  title     = {Quantitative proteomics using {SWATH-MS} identifies mechanisms of chloride tolerance in the halophilic acidophile \emph{{A}cidihalobacter prosperus} {DSM} 14174},
  year      = {2018},
  number    = {10},
  pages     = {638--648},
  volume    = {169},
  doi       = {10.1016/j.resmic.2018.07.002},
}

@Article{LTH+11,
  author    = {Lee, M Violet and Topper, Scott E and Hubler, Shane L and Hose, James and Wenger, Craig D and Coon, Joshua J and Gasch, Audrey P},
  journal   = {Molecular Systems Biology},
  title     = {A dynamic model of proteome changes reveals new roles for transcript alteration in yeast},
  year      = {2011},
  number    = {1},
  pages     = {514},
  volume    = {7},
  doi       = {10.1038/msb.2011.48},
}

@Article{AST+20,
  author    = {Syed Azmal Ali and Parul Singh and Sudhir K. Tomar and Ashok K. Mohanty and Pradip Behare},
  journal   = {Journal of Proteomics},
  title     = {Proteomics fingerprints of systemic mechanisms of adaptation to bile in \emph{{L}actobacillus fermentum}},
  year      = {2020},
  pages     = {103600},
  volume    = {213},
  doi       = {10.1016/j.jprot.2019.103600},
}

@Article{CCW+13,
  author    = {Chen, Xiulan and Cui, Ziyou and Wei, Shasha and Hou, Junjie and Xie, Zhensheng and Peng, Xue and Li, Jing and Cai, Tanxi and Hang, Haiying and Yang, Fuquan},
  journal   = {Proteomics},
  title     = {Chronic high glucose induced {INS}-1β cell mitochondrial dysfunction: {A} comparative mitochondrial proteome with {SILAC}},
  year      = {2013},
  number    = {20},
  pages     = {3030--3039},
  volume    = {13},
  doi       = {10.1002/pmic.201200448},
}

@Article{MHP+20,
  author    = {Erika Meneses-Romero and Lorena Hernández-Orihuela and Victoria Pando-Robles and Tomas D. López and Juan A. Oses-Prieto and Alma L. Burlingame and Cesar V.F. Batista},
  journal   = {Journal of Proteomics},
  title     = {Quantitative proteomic analysis reveals high interference on protein expression of {H9c2} cells activated with glucose and cardiotonic steroids},
  year      = {2020},
  pages     = {103536},
  volume    = {211},
  doi       = {10.1016/j.jprot.2019.103536},
}

@Article{MPR+20,
  author    = {Madonna, Rosalinda and Pieragostino, Damiana and Rossi, Claudia and Confalone, Pamela and Cicalini, Ilaria and Minnucci, Ilaria and Zucchelli, Mirco and Del Boccio, Piero and De Caterina, Raffaele},
  journal   = {Vascular Pharmacology},
  title     = {Simulated hyperglycemia impairs insulin signaling in endothelial cells through a hyperosmolar mechanism},
  year      = {2020},
  pages     = {106678},
  volume    = {130},
  doi       = {10.1016/j.vph.2020.106678},
}

@Article{SFKD17,
  author    = {Schmudlach, Andrew and Felton, Jeremy and Kennedy, Robert T. and Dovichi, Norman J.},
  journal   = {Analyst},
  title     = {Bottom-up proteomics analysis of the secretome of murine islets of {L}angerhans in elevated glucose levels},
  year      = {2017},
  pages     = {284--291},
  volume    = {142},
  doi       = {10.1039/C6AN02268E},
}

@Article{IXA+19,
  author    = {Irshad, Zehra and Xue, Mingzhan and Ashour, Amal and Larkin, James R. and Thornalley, Paul J. and Rabbani, Naila},
  journal   = {Scientific Reports},
  title     = {Activation of the unfolded protein response in high glucose treated endothelial cells is mediated by methylglyoxal},
  year      = {2019},
  number    = {1},
  pages     = {7889},
  volume    = {9},
  doi       = {10.1038/s41598-019-44358-1},
}

@Article{WFSL09,
  author    = {Wang, Xiao-Li and Fu, Alex and Spiro, Craig and Lee, Hon-Chi},
  journal   = {Journal of Proteomics \& Bioinformatics},
  title     = {Proteomic analysis of vascular endothelial cells: effects of laminar shear stress and high glucose},
  year      = {2009},
  number    = {10},
  pages     = {445--445},
  volume    = {2},
  doi       = {10.4172/jpb.1000104},
  url       = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818370/},
}

@Article{QHT+13,
  author    = {Qiao, Jianjun and Huang, Siqiang and Te, Rigen and Wang, Jiangxin and Chen, Lei and Zhang, Weiwen},
  journal   = {Applied Microbiology and Biotechnology},
  title     = {Integrated proteomic and transcriptomic analysis reveals novel genes and regulatory mechanisms involved in salt stress responses in \emph{{S}ynechocystis} sp. {PCC} 6803},
  year      = {2013},
  number    = {18},
  pages     = {8253--8264},
  volume    = {97},
  doi       = {10.1007/s00253-013-5139-8},
}

@Article{SAS+14,
  author    = {Ravi Kanth Rao Saini and Sanaz Attarha and {da Silva Santos}, Claire and Justyna Kolakowska and Keiko Funa and Serhiy Souchelnytskyi},
  journal   = {Biochemical and Biophysical Research Communications},
  title     = {Proteomics of dedifferentiation of {SK-N-BE2} neuroblastoma cells},
  year      = {2014},
  number    = {1},
  pages     = {202--209},
  volume    = {454},
  doi       = {10.1016/j.bbrc.2014.10.065},
}

@Article{LWS+19,
  author    = {Li, Mo and Wang, Qianqian and Song, Xuefei and Guo, Jingjing and Wu, Junrui and Wu, Rina},
  journal   = {Annals of Microbiology},
  title     = {{iTRAQ}-based proteomic analysis of responses of \emph{{L}actobacillus plantarum} FS5-5 to salt tolerance},
  year      = {2019},
  number    = {4},
  pages     = {377--394},
  volume    = {69},
  doi       = {10.1007/s13213-018-1425-0},
}

@Article{MFD+10,
  author    = {Maris, Michael and Ferreira, Gabriela B. and D’Hertog, Wannes and Cnop, Miriam and Waelkens, Etienne and Overbergh, Lut and Mathieu, Chantal},
  journal   = {Journal of Proteome Research},
  title     = {High glucose induces dysfunction in insulin secretory cells by different pathways: a proteomic approach},
  year      = {2010},
  number    = {12},
  pages     = {6274--6287},
  volume    = {9},
  doi       = {10.1021/pr100557w},
}

@Article{SFG+12,
  author    = {Schrimpe-Rutledge, Alexandra C. and Fontès, Ghislaine and Gritsenko, Marina A. and Norbeck, Angela D. and Anderson, David J. and Waters, Katrina M. and Adkins, Joshua N. and Smith, Richard D. and Poitout, Vincent and Metz, Thomas O.},
  journal   = {Journal of Proteome Research},
  title     = {Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using {LC–MS/MS}-based proteomics},
  year      = {2012},
  number    = {7},
  pages     = {3520--3532},
  volume    = {11},
  doi       = {10.1021/pr3002996},
}

@Article{PNWB09,
  author    = {Pandhal, Jagroop and Noirel, Josselin and Wright, Phillip C. and Biggs, Catherine A.},
  journal   = {Saline Systems},
  title     = {A systems biology approach to investigate the response of \emph{{S}ynechocystis} sp. {PCC6803} to a high salt environment},
  year      = {2009},
  number    = {1},
  pages     = {8},
  volume    = {5},
  doi       = {10.1186/1746-1448-5-8},
}

@Article{DTS+07,
  author    = {Dos Santos, Alexandre and Thiers, Valérie and Sar, Sokhavuth and Derian, Nicolas and Bensalem, Noura and Yilmaz, Funda and Bralet, Marie-Pierre and Ducot, Béatrice and Bréchot, Christian and Demaugre, France},
  journal   = {Proteomics - Clinical Applications},
  title     = {Contribution of laser microdissection-based technology to proteomic analysis in hepatocellular carcinoma developing on cirrhosis},
  year      = {2007},
  number    = {6},
  pages     = {545--554},
  volume    = {1},
  doi       = {10.1002/prca.200600474},
}

@Article{GBR+20,
  author    = {Floriane Gaucher and Sylvie Bonnassie and Houem Rabah and Pauline Leverrier and Sandrine Pottier and Julien Jardin and Valérie Briard-Bion and Pierre Marchand and Romain Jeantet and Philippe Blanc and Gwénaël Jan},
  journal   = {Data in Brief},
  title     = {Data from a proteomic analysis highlight different osmoadaptations in two strain of \emph{{P}ropionibacterium freudenreichii}},
  year      = {2020},
  pages     = {104932},
  volume    = {28},
  doi       = {10.1016/j.dib.2019.104932},
}

@Article{LFY+12,
  author    = {Li, Jinxi and Ferraris, Joan D. and Yu, Danni and Singh, Taruna and Izumi, Yuichiro and Wang, Guanghui and Gucek, Marjan and Burg, Maurice B.},
  journal   = {Physiological Genomics},
  title     = {Proteomic analysis of high {NaCl}-induced changes in abundance of nuclear proteins},
  year      = {2012},
  number    = {21},
  pages     = {1063--1071},
  volume    = {44},
  doi       = {10.1152/physiolgenomics.00068.2012},
}

@Article{BSG15,
  author    = {Borlak, Jürgen and Singh, Prashant and Gazzana, Giuseppe},
  journal   = {BMC Genomics},
  title     = {Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events},
  year      = {2015},
  number    = {1},
  pages     = {124},
  volume    = {16},
  doi       = {10.1186/s12864-015-1312-z},
}

@Article{RLA+10,
  author    = {Line Roy and Sylvie LaBoissière and Eman Abdou and Geneviève Thibault and Nathalie Hamel and Maryam Taheri and Daniel Boismenu and Joël Lanoix and Robert E. Kearney and Jacques Paiement},
  journal   = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
  title     = {Proteomic analysis of the transitional endoplasmic reticulum in hepatocellular carcinoma: {A}n organelle perspective on cancer},
  year      = {2010},
  number    = {9},
  pages     = {1869--1881},
  volume    = {1804},
  doi       = {10.1016/j.bbapap.2010.05.008},
}

@Article{SCL+20,
  author    = {Shin, Heon and Cha, Hyun-Jeong and Lee, Min Jung and Na, Keun and Park, Donha and Kim, Chae-Yeon and Han, Dai Hoon and Kim, Hoguen and Paik, Young-Ki},
  journal   = {Journal of Proteome Research},
  title     = {Identification of {ALDH6A1} as a potential molecular signature in hepatocellular carcinoma via quantitative profiling of the mitochondrial proteome},
  year      = {2020},
  number    = {4},
  pages     = {1684--1695},
  volume    = {19},
  doi       = {10.1021/acs.jproteome.9b00846},
}

@Article{GAM+16,
  author    = {Gamboni, Fabia and Anderson, Cameron and Mitra, Sanchayita and Reisz, Julie A. and Nemkov, Travis and Dzieciatkowska, Monika and Jones, Kenneth L. and Hansen, Kirk C. and D’Alessandro, Angelo and Banerjee, Anirban},
  journal   = {Journal of Proteome Research},
  title     = {Hypertonic saline primes activation of the p53–p21 signaling axis in human small airway epithelial cells that prevents inflammation induced by pro-inflammatory cytokines},
  year      = {2016},
  number    = {10},
  pages     = {3813--3826},
  volume    = {15},
  doi       = {10.1021/acs.jproteome.6b00602},
}

@Article{GZL+20,
  author    = {Gao, Huanhuan and Zhang, Fangfei and Liang, Shuang and Zhang, Qiushi and Lyu, Mengge and Qian, Liujia and Liu, Wei and Ge, Weigang and Chen, Chen and Yi, Xiao and Zhu, Jiang and Lu, Cong and Sun, Ping and Liu, Kexin and Zhu, Yi and Guo, Tiannan},
  journal   = {Journal of Proteome Research},
  title     = {Accelerated lysis and proteolytic digestion of biopsy-level fresh-frozen and {FFPE} tissue samples using pressure cycling technology},
  year      = {2020},
  number    = {5},
  pages     = {1982--1990},
  volume    = {19},
  doi       = {10.1021/acs.jproteome.9b00790},
}

@Article{HGC+18,
  author    = {Huang, Song and Gaucher, Floriane and Cauty, Chantal and Jardin, Julien and Le Loir, Yves and Jeantet, Romain and Chen, Xiao Dong and Jan, Gwénaël},
  journal   = {Frontiers in Microbiology},
  title     = {Growth in hyper-concentrated sweet whey triggers multi stress tolerance and spray drying survival in \emph{{L}actobacillus casei} {BL23}: from the molecular basis to new perspectives for sustainable probiotic production},
  year      = {2018},
  pages     = {2548},
  volume    = {9},
  doi       = {10.3389/fmicb.2018.02548},
}

@Article{SCG+15,
  author    = {Selevsek, Nathalie and Chang, Ching-Yun and Gillet, Ludovic C. and Navarro, Pedro and Bernhardt, Oliver M. and Reiter, Lukas and Cheng, Lin-Yang and Vitek, Olga and Aebersold, Ruedi},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {Reproducible and consistent quantification of the \emph{{S}accharomyces cerevisiae} proteome by {SWATH}-mass spectrometry},
  year      = {2015},
  number    = {3},
  pages     = {739--749},
  volume    = {14},
  doi       = {10.1074/mcp.M113.035550},
}

@Article{YXZ+18,
  author    = {Yang, Jing and Xie, Qi and Zhou, Hui and Chang, Lei and Wei, Wei and Wang, Yin and Li, Hong and Deng, Zixin and Xiao, Yuling and Wu, Junzhu and Xu, Ping and Hong, Xuechuan},
  journal   = {Journal of Proteome Research},
  title     = {Proteomic analysis and {NIR-II} imaging of {MCM2} protein in hepatocellular carcinoma},
  year      = {2018},
  number    = {7},
  pages     = {2428--2439},
  volume    = {17},
  doi       = {10.1021/acs.jproteome.8b00181},
}

@Article{SKV+16,
  author    = {Schmidt, Alexander and Kochanowski, Karl and Vedelaar, Silke and Ahrné, Erik and Volkmer, Benjamin and Callipo, Luciano and Knoops, Kèvin and Bauer, Manuel and Aebersold, Ruedi and Heinemann, Matthias},
  journal   = {Nature Biotechnology},
  title     = {The quantitative and condition-dependent \emph{{E}scherichia coli} proteome},
  year      = {2016},
  number    = {1},
  pages     = {104--110},
  volume    = {34},
  doi       = {10.1038/nbt.3418},
}

@Article{ADW+14,
  author    = {An, Haoran and Douillard, Fran{\c c}ois P. and Wang, Guohong and Zhai, Zhengyuan and Yang, Jin and Song, Shuhui and Cui, Jianyun and Ren, Fazheng and Luo, Yunbo and Zhang, Bing and Hao, Yanling},
  journal   = {Molecular \& Cellular Proteomics},
  title     = {Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic \emph{{B}ifidobacterium longum} {BBMN68}},
  year      = {2014},
  number    = {10},
  pages     = {2558--2572},
  volume    = {13},
  doi       = {10.1074/mcp.M114.039156},
}

@Article{KKG+14,
  author    = {Kocharunchitt, Chawalit and King, Thea and Gobius, Kari and Bowman, John P. and Ross, Tom},
  journal   = {PLOS One},
  title     = {Global genome response of \emph{{E}scherichia coli} {O157:H7} {S}akai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity},
  year      = {2014},
  number    = {3},
  pages     = {e90422},
  volume    = {9},
  doi       = {10.1371/journal.pone.0090422},
}

@Article{FGW+12,
  author    = {Fan, Nai-Jun and Gao, Chun-Fang and Wang, Chang-Song and Lv, Jing-Jing and Zhao, Guang and Sheng, Xin-Hua and Wang, Xiu-Li and Li, Dong-Hui and Liu, Qing-Yin and Yin, Jian},
  journal   = {Canadian Journal of Gastroenterology},
  title     = {Discovery and verification of gelsolin as a potential biomarker of colorectal adenocarcinoma in a {C}hinese population: {Examining} differential protein expression using an {iTRAQ} labelling-based proteomics approach},
  year      = {2012},
  number    = {1},
  pages     = {41--47},
  volume    = {26},
  doi       = {10.1155/2012/645218},
}

@Article{MHN+08,
  author    = {Mao, Lei and Hartl, Daniela and Nolden, Tobias and Koppelstätter, Andrea and Klose, Joachim and Himmelbauer, Heinz and Zabel, Claus},
  journal   = {Journal of Proteome Research},
  title     = {Pronounced alterations of cellular metabolism and structure due to hyper- or hypo-osmosis},
  year      = {2008},
  number    = {9},
  pages     = {3968--3983},
  volume    = {7},
  doi       = {10.1021/pr800245x},
}

@Article{TSC18,
  author    = {Tien, Matthew Z. and Stein, Benjamin J. and Crosson, Sean},
  journal   = {Journal of Bacteriology},
  title     = {Coherent feedforward regulation of gene expression by \emph{{C}aulobacter} σ\textsuperscript{T} and {GsrN} during hyperosmotic stress},
  year      = {2018},
  number    = {19},
  pages     = {e00349-18},
  volume    = {200},
  doi       = {10.1128/JB.00349-18},
}

@Article{PBP+14,
  author    = {Pittman, Joseph R. and Buntyn, Joe O. and Posadas, Gabriel and Nanduri, Bindu and Pendarvis, Ken and Donaldson, Janet R.},
  journal   = {Journal of Proteome Research},
  title     = {Proteomic analysis of cross protection provided between cold and osmotic stress in \emph{{L}isteria monocytogenes}},
  year      = {2014},
  number    = {4},
  pages     = {1896--1904},
  volume    = {13},
  doi       = {10.1021/pr401004a},
}

@Article{DKM+20,
  author    = {Doron, Gilad and Klontzas, Michail E. and Mantalaris, Athanasios and Guldberg, Robert E. and Temenoff, Johnna S.},
  journal   = {Biotechnology and Bioengineering},
  title     = {Multiomics characterization of mesenchymal stromal cells cultured in monolayer and as aggregates},
  year      = {2020},
  number    = {6},
  pages     = {1761--1778},
  volume    = {117},
  doi       = {10.1002/bit.27317},
}

@Article{BTX+17,
  author    = {Burger, Dylan and Turner, Maddison and Xiao, Fengxia and Munkonda, Mercedes N. and Akbari, Shareef and Burns, Kevin D.},
  journal   = {Diabetologia},
  title     = {High glucose increases the formation and pro-oxidative activity of endothelial microparticles},
  year      = {2017},
  number    = {9},
  pages     = {1791--1800},
  volume    = {60},
  doi       = {10.1007/s00125-017-4331-2},
}

@Article{ZKL+20,
  author    = {Zhang, Jinhui and Kim, Sangyub and Li, Li and Kemp, Christopher J. and Jiang, Cheng and Lü, Junxuan},
  journal   = {The Prostate},
  title     = {Proteomic and transcriptomic profiling of \emph{{P}ten} gene-knockout mouse model of prostate cancer},
  year      = {2020},
  number    = {7},
  pages     = {588--605},
  volume    = {80},
  doi       = {10.1002/pros.23972},
}

@Article{KPS+20,
  author    = {Kelemen, Olga and Pla, Indira and Sanchez, Aniel and Rezeli, Melinda and Szasz, Attila Marcell and Malm, Johan and Laszlo, Viktoria and Kwon, Ho Jeong and Dome, Balazs and Marko-Varga, Gyorgy},
  journal   = {Clinical and Translational Medicine},
  title     = {Proteomic analysis enables distinction of early- versus advanced-stage lung adenocarcinomas},
  year      = {2020},
  number    = {2},
  pages     = {e106},
  volume    = {10},
  doi       = {10.1002/ctm2.106},
}

@Article{LDM+20,
  author    = {Latosinska, Agnieszka and Davalieva, Katarina and Makridakis, Manousos and Mullen, William and Schanstra, Joost P. and Vlahou, Antonia and Mischak, Harald and Frantzi, Maria},
  journal   = {Diagnostics},
  title     = {Molecular changes in tissue proteome during prostate cancer development: Proof-of-principle investigation},
  year      = {2020},
  number    = {9},
  pages     = {655},
  volume    = {10},
  doi       = {10.3390/diagnostics10090655},
}

@Article{XZW+20,
  author    = {Jun-Yu Xu and Chunchao Zhang and Xiang Wang and Linhui Zhai and Yiming Ma and Yousheng Mao and Kun Qian and Changqing Sun and Zhiwei Liu and Shangwen Jiang and Minghui Wang and Lin Feng and Lei Zhao and Ping Liu and Bo Wang and Xin Zhao and Hui Xie and Xiaoyun Yang and Liyuan Zhao and Yafei Chang and Jingya Jia and Xijun Wang and Yimin Zhang and Yaru Wang and Yikun Yang and Zhixiang Wu and Longhai Yang and Bin Liu and Teng Zhao and Shengguo Ren and Aihua Sun and Yang Zhao and Wantao Ying and Fei Wang and Guangshun Wang and Yi Zhang and Shujun Cheng and Jun Qin and Xiaohong Qian and Yi Wang and Jing Li and Fuchu He and Ting Xiao and Minjia Tan},
  journal   = {Cell},
  title     = {Integrative proteomic characterization of human lung adenocarcinoma},
  year      = {2020},
  number    = {1},
  pages     = {245--261},
  volume    = {182},
  doi       = {10.1016/j.cell.2020.05.043},
}

@Article{LLF+20,
  author    = {Lin, Yuxiang and Lin, Ling and Fu, Fangmeng and Wang, Chuan and Hu, Anqi and Xie, Juanjuan and Jiang, Meichen and Wang, Zhenxin and Yang, Lujie and Guo, Rongrong and Yang, Pengyuan and Shen, Huali},
  journal   = {Breast Cancer Research and Treatment},
  title     = {Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer},
  year      = {2020},
  doi       = {10.1007/s10549-020-05916-8},
}

@Article{ZZX+20,
  author    = {Tiansheng Zhu and Yi Zhu and Yue Xuan and Huanhuan Gao and Xue Cai and Sander R. Piersma and Thang V. Pham and Tim Schelfhorst and Richard R.G.D. Haas and Irene V. Bijnsdorp and Rui Sun and Liang Yue and Guan Ruan and Qiushi Zhang and Mo Hu and Yue Zhou and Winan J. {Van Houdt} and Tessa Y.S. {Le Large} and Jacqueline Cloos and Anna Wojtuszkiewicz and Danijela Koppers-Lalic and Franziska Böttger and Chantal Scheepbouwer and Ruud H. Brakenhoff and Geert J.L.H. {van Leenders} and Jan N.M. Ijzermans and John W.M. Martens and Renske D.M. Steenbergen and Nicole C. Grieken and Sathiyamoorthy Selvarajan and Sangeeta Mantoo and Sze S. Lee and Serene J.Y. Yeow and Syed M.F. Alkaff and Nan Xiang and Yaoting Sun and Xiao Yi and Shaozheng Dai and Wei Liu and Tian Lu and Zhicheng Wu and Xiao Liang and Man Wang and Yingkuan Shao and Xi Zheng and Kailun Xu and Qin Yang and Yifan Meng and Cong Lu and Jiang Zhu and Jin'e Zheng and Bo Wang and Sai Lou and Yibei Dai and Chao Xu and Chenhuan Yu and Huazhong Ying and Tony K. Lim and Jianmin Wu and Xiaofei Gao and Zhongzhi Luan and Xiaodong Teng and Peng Wu and Shi'ang Huang and Zhihua Tao and Narayanan G. Iyer and Shuigeng Zhou and Wenguang Shao and Henry Lam and Ding Ma and Jiafu Ji and Oi L. Kon and Shu Zheng and Ruedi Aebersold and Connie R. Jimenez and Tiannan Guo},
  journal   = {Genomics, Proteomics \& Bioinformatics},
  title     = {{DPHL}: {A} {DIA} pan-human protein mass spectrometry library for robust biomarker discovery},
  year      = {2020},
  doi       = {10.1016/j.gpb.2019.11.008},
}
