Eric W Deutsch - Publications

Affiliations: 
Institute for Systems Biology, Seattle, Seattle, WA, United States 
Area:
Computational Proteomics

190 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. Journal of Proteome Research. PMID 34672606 DOI: 10.1021/acs.jproteome.1c00657  1
2021 Omenn GS, Lane L, Overall CM, Paik YK, Cristea IM, Corrales FJ, Lindskog C, Weintraub S, Roehrl MHA, Liu S, Bandeira N, Srivastava S, Chen YJ, Aebersold R, Moritz RL, ... Deutsch EW, et al. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research. PMID 34670092 DOI: 10.1021/acs.jproteome.1c00590  1
2021 Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, ... ... Deutsch EW, et al. A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications. 12: 5854. PMID 34615866 DOI: 10.1038/s41467-021-26111-3  1
2021 van Wijk KJ, Leppert T, Sun Q, Boguraev SS, Sun Z, Mendoza L, Deutsch EW. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. The Plant Cell. PMID 34411258 DOI: 10.1093/plcell/koab211  1
2021 Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, et al. Universal Spectrum Identifier for mass spectra. Nature Methods. PMID 34183830 DOI: 10.1038/s41592-021-01184-6  1
2021 Schmidt T, Samaras P, Dorfer V, Panse C, Kockmann T, Bichmann L, van Puyvelde B, Perez-Riverol Y, Deutsch EW, Kuster B, Wilhelm M. Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. Journal of Proteome Research. 20: 3388-3394. PMID 33970638 DOI: 10.1021/acs.jproteome.1c00096  1
2021 Reales-Calderón JA, Sun Z, Mascaraque V, Pérez-Navarro E, Vialás V, Deutsch EW, Moritz RL, Gil C, Martínez JL, Molero G. A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen. Journal of Proteomics. 104192. PMID 33757883 DOI: 10.1016/j.jprot.2021.104192  1
2021 Bandeira N, Deutsch EW, Kohlbacher O, Martens L, Vizcaíno JA. Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future. Molecular & Cellular Proteomics : McP. 100071. PMID 33711481 DOI: 10.1016/j.mcpro.2021.100071  1
2020 Vizcaíno JA, Kubiniok P, Kovalchik KA, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E. The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases. Molecular & Cellular Proteomics : McP. 19: 31-49. PMID 33451557 DOI: 10.1074/mcp.R119.001743  1
2020 Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, et al. A high-stringency blueprint of the human proteome. Nature Communications. 11: 5301. PMID 33067450 DOI: 10.1038/s41467-020-19045-9  1
2020 Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, ... Deutsch EW, et al. Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project. Journal of Proteome Research. PMID 32931287 DOI: 10.1021/Acs.Jproteome.0C00485  1
2020 Bhamber RS, Jankevics A, Deutsch EW, Jones AR, Dowsey AW. mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements. Journal of Proteome Research. PMID 32864978 DOI: 10.1021/Acs.Jproteome.0C00192  1
2020 Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, ... ... Deutsch EW, et al. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000research. 9: 136. PMID 32308977 DOI: 10.12688/F1000Research.18236.1  1
2020 Eng JK, Deutsch EW. Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis using the PSI Extended FASTA Format (PEFF). Proteomics. e1900362. PMID 32106352 DOI: 10.1002/Pmic.201900362  1
2019 Paik YK, Overall CM, Corrales F, Deutsch EW, Lane L, Omenn GS. Advances in Identifying and Characterizing the Human Proteome. Journal of Proteome Research. 18: 4079-4084. PMID 31805768 DOI: 10.1021/Acs.Jproteome.9B00745  1
2019 Vizcaíno JA, Kubiniok P, Kovalchik K, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E. The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases. Molecular & Cellular Proteomics : McP. PMID 31744855 DOI: 10.1074/Mcp.R119.001743  1
2019 Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, et al. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Research. PMID 31686107 DOI: 10.1093/Nar/Gkz984  1
2019 Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. Journal of Proteome Research. PMID 31599596 DOI: 10.1021/Acs.Jproteome.9B00542  1
2019 Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM. Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. Journal of Proteome Research. PMID 31573204 DOI: 10.1021/Acs.Jproteome.9B00503  1
2019 Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018-2019 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research. PMID 31430157 DOI: 10.1021/Acs.Jproteome.9B00434  1
2019 Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL. PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. Journal of Proteome Research. PMID 31290668 DOI: 10.1021/Acs.Jproteome.9B00205  1
2019 Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, ... ... Deutsch EW, et al. Proteomics Standards Initiative Extended FASTA Format (PEFF). Journal of Proteome Research. PMID 31081335 DOI: 10.1021/Acs.Jproteome.9B00064  1
2019 Madduri R, Chard K, D'Arcy M, Jung SC, Rodriguez A, Sulakhe D, Deutsch E, Funk C, Heavner B, Richards M, Shannon P, Glusman G, Price N, Kesselman C, Foster I. Reproducible big data science: A case study in continuous FAIRness. Plos One. 14: e0213013. PMID 30973881 DOI: 10.1371/Journal.Pone.0213013  1
2018 Paik YK, Overall CM, Corrales F, Deutsch EW, Lane L, Omenn GS. Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. Journal of Proteome Research. 17: 4023-4030. PMID 30985145 DOI: 10.1021/Acs.Jproteome.8B00885  1
2018 Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather ND, Deutsch EW, Kappe SHI, Moritz RL. A tandem mass spectrometry sequence database search method for identification of O-fucosylated proteins by mass spectrometry. Journal of Proteome Research. PMID 30523691 DOI: 10.1021/Acs.Jproteome.8B00638  1
2018 Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, et al. Expanding the use of spectral libraries in proteomics. Journal of Proteome Research. PMID 30270626 DOI: 10.1021/Acs.Jproteome.8B00485  1
2018 Mendoza L, Deutsch EW, Sun Z, Campbell DS, Shteynberg DD, Moritz RL. Flexible and fast mapping of peptides to a proteome with ProteoMapper. Journal of Proteome Research. PMID 30230343 DOI: 10.1021/Acs.Jproteome.8B00544  1
2018 Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research. PMID 30099871 DOI: 10.1021/Acs.Jproteome.8B00441  1
2018 Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E. A tissue-based draft map of the murine MHC class I immunopeptidome. Scientific Data. 5: 180157. PMID 30084848 DOI: 10.1038/Sdata.2018.157  1
2018 Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA. The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology. 19: 12. PMID 29386051 DOI: 10.1186/S13059-017-1377-X  1
2017 Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, ... ... Deutsch EW, et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Medicine. 9: 113. PMID 29254494 DOI: 10.1186/S13073-017-0509-Y  1
2017 Paik YK, Overall CM, Deutsch EW, Van Eyk JE, Omenn GS. Progress and Future Direction of Chromosome-Centric Human Proteome Project. Journal of Proteome Research. 16: 4253-4258. PMID 29191025 DOI: 10.1021/Acs.Jproteome.7B00734  1
2017 Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, ... ... Deutsch EW, et al. The SysteMHC Atlas project. Nucleic Acids Research. PMID 28985418 DOI: 10.1093/Nar/Gkx664  1
2017 Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. Journal of Proteome Research. PMID 28938075 DOI: 10.1021/Acs.Jproteome.7B00467  1
2017 Michalik S, Depke M, Murr A, Gesell Salazar M, Kusebauch U, Sun Z, Meyer TC, Surmann K, Pförtner H, Hildebrandt P, Weiss S, Palma Medina LM, Gutjahr M, Hammer E, Becher D, ... ... Deutsch EW, et al. A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions. Scientific Reports. 7: 9718. PMID 28887440 DOI: 10.1038/S41598-017-10059-W  1
2017 Omenn GS, Lane L, Lundberg EK, Overall CM, Deutsch EW. Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. Journal of Proteome Research. PMID 28853897 DOI: 10.1021/Acs.Jproteome.7B00375  1
2017 Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, et al. The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. Journal of Proteome Research. PMID 28849660 DOI: 10.1021/Acs.Jproteome.7B00370  1
2017 Vizcaíno JA, Mayer G, Perkins SR, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, ... ... Deutsch EW, et al. The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics : McP. PMID 28515314 DOI: 10.1074/Mcp.M117.068429  1
2017 Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, ... Deutsch EW, et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nature Biotechnology. 35: 406-409. PMID 28486464 DOI: 10.1038/Nbt.3790  1
2017 Abbatiello SE, Ackermann BL, Borchers CH, Bradshaw RA, Carr SA, Chalkley RJ, Choi M, Deutsch EW, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss MJ, MacLean B, et al. New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins. Molecular & Cellular Proteomics : McP. PMID 28183812 DOI: 10.1074/Mcp.E117.067801  1
2017 McCord JP, Sun Z, Deutsch EW, Moritz RL, Muddiman DC. The PeptideAtlas of the Domestic Laying Hen. Journal of Proteome Research. PMID 28166638 DOI: 10.1021/Acs.Jproteome.6B00952  1
2017 Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, ... Deutsch EW, et al. Building ProteomeTools based on a complete synthetic human proteome. Nature Methods. PMID 28135259 DOI: 10.1038/Nmeth.4153  1
2016 Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, et al. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Research. PMID 27924013 DOI: 10.1093/Nar/Gkw936  1
2016 Paik YK, Overall CM, Deutsch EW, Hancock WS, Omenn GS. Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV. Journal of Proteome Research. 15: 3945-3950. PMID 27809547 DOI: 10.1021/Acs.Jproteome.6B00803  1
2016 Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL. Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. Journal of Proteome Research. PMID 27577934 DOI: 10.1021/Acs.Jproteome.6B00445  1
2016 Van Eyk JE, Corrales FJ, Aebersold R, Cerciello F, Deutsch EW, Roncada P, Sanchez JC, Yamamoto T, Yang P, Zhang H, Omenn GS. Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. Journal of Proteome Research. 15: 3979-3987. PMID 27573249 DOI: 10.1021/Acs.Jproteome.6B00444  1
2016 Dinov ID, Heavner B, Tang M, Glusman G, Chard K, Darcy M, Madduri R, Pa J, Spino C, Kesselman C, Foster I, Deutsch EW, Price ND, Van Horn JD, Ames J, et al. Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations. Plos One. 11: e0157077. PMID 27494614 DOI: 10.1371/Journal.Pone.0157077  1
2016 Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. Journal of Proteome Research. 15: 3961-3970. PMID 27490519 DOI: 10.1021/Acs.Jproteome.6B00392  1
2016 Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. Journal of Proteome Research. PMID 27487407 DOI: 10.1021/Acs.Jproteome.6B00511  1
2016 Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL. An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results. Journal of the American Society For Mass Spectrometry. PMID 27469004 DOI: 10.1007/S13361-016-1435-8  1
2016 Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. PMID 27453469 DOI: 10.1016/J.Cell.2016.06.041  1
2015 Hesselager MO, Codrea MC, Sun Z, Deutsch EW, Bennike TB, Stensballe A, Bundgaard L, Moritz RL, Bendixen E. The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine. Proteomics. PMID 26699206 DOI: 10.1002/Pmic.201500195  1
2015 Vialas V, Sun Z, Reales-Calderón JA, Hernáez ML, Casas V, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Moritz RL, Gil C. A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage. Journal of Proteomics. PMID 26493587 DOI: 10.1016/J.Jprot.2015.10.019  1
2015 Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra. Journal of the American Society For Mass Spectrometry. PMID 26419769 DOI: 10.1007/S13361-015-1252-5  1
2015 Paik YK, Omenn GS, Overall CM, Deutsch EW, Hancock WS. Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. Journal of Proteome Research. 14: 3409-14. PMID 26337862 DOI: 10.1021/Acs.Jproteome.5B00785  1
2015 Toga AW, Foster I, Kesselman C, Madduri R, Chard K, Deutsch EW, Price ND, Glusman G, Heavner BD, Dinov ID, Ames J, Van Horn J, Kramer R, Hood L. Big Biomedical data as the key resource for discovery science. Journal of the American Medical Informatics Association : Jamia. PMID 26198305 DOI: 10.1093/Jamia/Ocv077  1
2015 Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. Journal of Proteome Research. 14: 3452-60. PMID 26155816 DOI: 10.1021/Acs.Jproteome.5B00499  1
2015 Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, ... Deutsch EW, et al. An open-source computational and data resource to analyze digital maps of immunopeptidomes. Elife. 4. PMID 26154972 DOI: 10.7554/Elife.07661  1
2015 Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS, Moritz RL. State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. Journal of Proteome Research. PMID 26139527 DOI: 10.1021/Acs.Jproteome.5B00500  1
2015 Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, ... Deutsch EW, et al. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. Journal of Proteome Research. PMID 26076068 DOI: 10.1021/Pr5013009  1
2015 Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H. Development of data representation standards by the human proteome organization proteomics standards initiative. Journal of the American Medical Informatics Association : Jamia. 22: 495-506. PMID 25726569 DOI: 10.1093/Jamia/Ocv001  1
2015 Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics. Clinical Applications. 9: 745-54. PMID 25631240 DOI: 10.1002/Prca.201400164  1
2015 Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline. Molecular & Cellular Proteomics : McP. 14: 399-404. PMID 25418363 DOI: 10.1074/Mcp.O114.043380  1
2015 Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Arlehamn CSL, Koh CC, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, ... ... Deutsch EW, et al. Author response: An open-source computational and data resource to analyze digital maps of immunopeptidomes Elife. DOI: 10.7554/Elife.07661.032  1
2014 Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, ... Deutsch EW, et al. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data. 1: 140031. PMID 25977788 DOI: 10.1038/Sdata.2014.31  1
2014 Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H. Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany. Proteomics. 14: 2363-8. PMID 25297050 DOI: 10.1002/Pmic.201470164  1
2014 Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL. Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 46: 13.25.1-13.25.28. PMID 24939129 DOI: 10.1002/0471250953.Bi1325S46  1
2014 Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology. 32: 223-6. PMID 24727771 DOI: 10.1038/Nbt.2839  1
2014 Teleman J, Dowsey AW, Gonzalez-Galarza FF, Perkins S, Pratt B, Röst HL, Malmström L, Malmström J, Jones AR, Deutsch EW, Levander F. Numerical compression schemes for proteomics mass spectrometry data. Molecular & Cellular Proteomics : McP. 13: 1537-42. PMID 24677029 DOI: 10.1074/Mcp.O114.037879  1
2014 Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular & Cellular Proteomics : McP. 13: 907-17. PMID 24443746 DOI: 10.1074/Mcp.M113.036095  1
2014 Bundgaard L, Jacobsen S, Sørensen MA, Sun Z, Deutsch EW, Moritz RL, Bendixen E. The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research. Proteomics. 14: 763-73. PMID 24436130 DOI: 10.1002/Pmic.201300398  1
2014 Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. Journal of Proteome Research. 13: 15-20. PMID 24364385 DOI: 10.1021/Pr401144X  1
2014 Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL. State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. Journal of Proteome Research. 13: 60-75. PMID 24261998 DOI: 10.1021/Pr4010037  1
2014 Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX. Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture. Molecular & Cellular Proteomics : McP. 13: 360-71. PMID 24187338 DOI: 10.1074/Mcp.M113.032813  1
2014 Vialas V, Sun Z, Loureiro y Penha CV, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Aebersold R, Moritz RL, Gil C. A Candida albicans PeptideAtlas. Journal of Proteomics. 97: 62-8. PMID 23811049 DOI: 10.1016/J.Jprot.2013.06.020  1
2014 Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochimica Et Biophysica Acta. 1844: 98-107. PMID 23429179 DOI: 10.1016/J.Bbapap.2013.02.017  1
2013 Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H. Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK. Proteomics. 13: 2931-7. PMID 24108681 DOI: 10.1002/Pmic.201370166  1
2013 Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW. Combining results of multiple search engines in proteomics. Molecular & Cellular Proteomics : McP. 12: 2383-93. PMID 23720762 DOI: 10.1074/Mcp.R113.027797  1
2013 Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, et al. The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Molecular & Cellular Proteomics : McP. 12: 2332-40. PMID 23599424 DOI: 10.1074/Mcp.O113.028506  1
2013 Martínez-Bartolomé S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernáez ML, et al. Guidelines for reporting quantitative mass spectrometry based experiments in proteomics Journal of Proteomics. 95: 84-88. PMID 23500130 DOI: 10.1016/J.Jprot.2013.02.026  1
2013 Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, et al. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database : the Journal of Biological Databases and Curation. 2013: bat009. PMID 23482073 DOI: 10.1093/Database/Bat009  1
2013 Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature. 494: 266-70. PMID 23334424 DOI: 10.1038/Nature11835  1
2013 Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, et al. A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. Journal of Proteome Research. 12: 45-57. PMID 23259914 DOI: 10.1021/Pr300985J  1
2013 Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL. The state of the human proteome in 2012 as viewed through PeptideAtlas. Journal of Proteome Research. 12: 162-71. PMID 23215161 DOI: 10.1021/Pr301012J  1
2012 Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J. Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. Bmc Bioinformatics. 13: 324. PMID 23216909 DOI: 10.1186/1471-2105-13-324  1
2012 Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, ... ... Deutsch EW, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology. 30: 918-20. PMID 23051804 DOI: 10.1038/Nbt.2377  1
2012 Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H. Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics. 12: 2767-72. PMID 22969026 DOI: 10.1002/Pmic.201270126  1
2012 Deutsch EW. File formats commonly used in mass spectrometry proteomics. Molecular & Cellular Proteomics : McP. 11: 1612-21. PMID 22956731 DOI: 10.1074/Mcp.R112.019695  0.01
2012 Killcoyne S, Handcock J, Robinson T, Deutsch EW, Boyle J. Interfaces to PeptideAtlas: a case study of standard data access systems. Briefings in Bioinformatics. 13: 615-26. PMID 22941959 DOI: 10.1093/bib/bbr067  1
2012 Bislev SL, Deutsch EW, Sun Z, Farrah T, Aebersold R, Moritz RL, Bendixen E, Codrea MC. A Bovine PeptideAtlas of milk and mammary gland proteomes. Proteomics. 12: 2895-9. PMID 22837157 DOI: 10.1002/Pmic.201200057  1
2012 Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science Translational Medicine. 4: 142ra94. PMID 22786679 DOI: 10.1126/Scitranslmed.3003989  1
2012 Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, ... ... Deutsch EW, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology. 30: 221-3. PMID 22398612 DOI: 10.1038/Nbt.2152  1
2012 Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & Cellular Proteomics : McP. 11: M111.014381. PMID 22375074 DOI: 10.1074/Mcp.M111.014381  1
2012 Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL. PASSEL: the PeptideAtlas SRMexperiment library. Proteomics. 12: 1170-5. PMID 22318887 DOI: 10.1002/Pmic.201100515  1
2012 Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H. From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland. Proteomics. 12: 351-5. PMID 22290802 DOI: 10.1002/Pmic.201290016  1
2012 Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, et al. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics. 12: 340-5. PMID 22290800 DOI: 10.1002/Pmic.201290014  1
2012 Killcoyne S, Deutsch EW, Boyle J. Mining PeptideAtlas for biomarkers and therapeutics in human disease. Current Pharmaceutical Design. 18: 748-54. PMID 22236120 DOI: 10.2174/138161212799277833  1
2012 Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY. TraML--a standard format for exchange of selected reaction monitoring transition lists. Molecular & Cellular Proteomics : McP. 11: R111.015040. PMID 22159873 DOI: 10.1074/Mcp.R111.015040  1
2012 Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. 12: 11-20. PMID 22069307 DOI: 10.1002/Pmic.201100562  1
2012 Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Journal of Proteome Research. 11: 1412-9. PMID 22053864 DOI: 10.1021/Pr201071T  0.01
2011 Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. Clinical Applications. 5: 580-9. PMID 22213554 DOI: 10.1002/prca.201100097  1
2011 Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Molecular & Cellular Proteomics : McP. 10: O111.015446. PMID 22052993 DOI: 10.1074/Mcp.O111.015446  0.01
2011 Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H. Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics. 11: 4284-90. PMID 22045680 DOI: 10.1002/Pmic.201190117  1
2011 Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L. jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. Journal of Proteome Research. 10: 5260-3. PMID 21967198 DOI: 10.1021/Pr200664H  1
2011 Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & Cellular Proteomics : McP. 10: M111.007690. PMID 21876204 DOI: 10.1074/Mcp.M111.007690  1
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, et al. The human proteome project: current state and future direction. Molecular & Cellular Proteomics : McP. 10: M111.009993. PMID 21742803 DOI: 10.1074/Mcp.M111.009993  1
2011 Chan QW, Parker R, Sun Z, Deutsch EW, Foster LJ. A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. Bmc Genomics. 12: 290. PMID 21639908 DOI: 10.1186/1471-2164-12-290  1
2011 Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & Cellular Proteomics : McP. 10: M110.006353. PMID 21632744 DOI: 10.1074/Mcp.M110.006353  1
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, et al. The human proteome project: Current state and future direction. Molecular & Cellular Proteomics : McP. PMID 21531903 DOI: 10.1074/mcp.O111.009993  1
2011 Farrah T, Deutsch EW, Aebersold R. Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods in Molecular Biology (Clifton, N.J.). 728: 349-74. PMID 21468960 DOI: 10.1007/978-1-61779-068-3_23  1
2011 Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. Bmc Bioinformatics. 12: 78. PMID 21414234 DOI: 10.1186/1471-2105-12-78  1
2011 Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA. Data standards for Omics data: the basis of data sharing and reuse. Methods in Molecular Biology (Clifton, N.J.). 719: 31-69. PMID 21370078 DOI: 10.1007/978-1-61779-027-0_2  1
2011 Deutsch EW. Tandem mass spectrometry spectral libraries and library searching. Methods in Molecular Biology (Clifton, N.J.). 696: 225-32. PMID 21063950 DOI: 10.1007/978-1-60761-987-1_13  0.01
2011 Turewicz M, Deutsch EW. Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output. Methods in Molecular Biology (Clifton, N.J.). 696: 179-203. PMID 21063948 DOI: 10.1007/978-1-60761-987-1_11  0.01
2011 Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, ... ... Deutsch EW, et al. mzML--a community standard for mass spectrometry data. Molecular & Cellular Proteomics : McP. 10: R110.000133. PMID 20716697 DOI: 10.1074/Mcp.R110.000133  0.01
2010 Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H. implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics. 10: 1895-8. PMID 20623474 DOI: 10.1002/Pmic.201090034  1
2010 Handcock J, Deutsch EW, Boyle J. mspecLINE: bridging knowledge of human disease with the proteome. Bmc Medical Genomics. 3: 7. PMID 20219133 DOI: 10.1186/1755-8794-3-7  1
2010 Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. A guided tour of the Trans-Proteomic Pipeline. Proteomics. 10: 1150-9. PMID 20101611 DOI: 10.1002/Pmic.200900375  1
2010 Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R. Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics. 10: 1190-5. PMID 20082347 DOI: 10.1002/Pmic.200900567  1
2010 Deutsch EW. Mass spectrometer output file format mzML. Methods in Molecular Biology (Clifton, N.J.). 604: 319-31. PMID 20013381 DOI: 10.1007/978-1-60761-444-9_22  0.01
2010 Deutsch EW. The PeptideAtlas Project. Methods in Molecular Biology (Clifton, N.J.). 604: 285-96. PMID 20013378 DOI: 10.1007/978-1-60761-444-9_19  0.01
2010 Lam H, Deutsch EW, Aebersold R. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. Journal of Proteome Research. 9: 605-10. PMID 19916561 DOI: 10.1021/Pr900947U  1
2009 Beck M, Malmström JA, Lange V, Schmidt A, Deutsch EW, Aebersold R. Visual proteomics of the human pathogen Leptospira interrogans. Nature Methods. 6: 817-23. PMID 19838170 DOI: 10.1038/Nmeth.1390  1
2009 Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H. Annual spring meeting of the proteomics standards initiative Proteomics. 9: 4429-4432. PMID 19670378 DOI: 10.1002/Pmic.200900407  1
2009 Malmström J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature. 460: 762-5. PMID 19606093 DOI: 10.1038/Nature08184  1
2009 Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N, Aebersold R, Lam H, Martin DB. MaRiMba: a software application for spectral library-based MRM transition list assembly. Journal of Proteome Research. 8: 4396-405. PMID 19603829 DOI: 10.1021/Pr900010H  1
2009 Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS. Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular Systems Biology. 5: 285. PMID 19536208 DOI: 10.1038/Msb.2009.42  1
2009 Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nature Methods. 6: 423-30. PMID 19448641 DOI: 10.1038/Nmeth.1333  1
2009 Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, Aebersold R, Hafen E. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. Bmc Bioinformatics. 10: 59. PMID 19210778 DOI: 10.1186/1471-2105-10-59  1
2009 Brusniak M, Campbell D, Chen J, Christiansen M, Deutsch E, Kwok C, Letarte S, Ramos H, Picotti P, Reiter L, Watts J, Aebersold R. ATAQS Computational Software Tool for High Throughput Transition Optimization and Validation for SRM Molecular & Cellular Proteomics. 8. DOI: 10.1074/Mcp.S801208-Mcp200  1
2008 Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R. A database of mass spectrometric assays for the yeast proteome. Nature Methods. 5: 913-4. PMID 18974732 DOI: 10.1038/Nmeth1108-913  1
2008 Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H. Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain Proteomics. 8: 4168-4172. PMID 18814335 DOI: 10.1002/Pmic.200800555  1
2008 Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. Building consensus spectral libraries for peptide identification in proteomics. Nature Methods. 5: 873-5. PMID 18806791 DOI: 10.1038/Nmeth.1254  1
2008 Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. 26: 889-96. PMID 18688244 DOI: 10.1038/Nbt.1411  1
2008 Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA, Nickson J, et al. Guidelines for reporting the use of mass spectrometry in proteomics. Nature Biotechnology. 26: 860-1. PMID 18688232 DOI: 10.1038/Nbt0808-860  1
2008 Deutsch E. mzML: A single, unifying data format for mass spectrometer output Proteomics. 8: 2776-2777. PMID 18655045 DOI: 10.1002/Pmic.200890049  1
2008 Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of Proteome Research. 7: 3755-64. PMID 18652504 DOI: 10.1021/Pr800031F  1
2008 Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, et al. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biology. 9: R93. PMID 18522751 DOI: 10.1186/Gb-2008-9-6-R93  1
2008 Pascal LE, True LD, Campbell DS, Deutsch EW, Risk M, Coleman IM, Eichner LJ, Nelson PS, Liu AY. Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. Bmc Genomics. 9: 246. PMID 18501003 DOI: 10.1186/1471-2164-9-246  1
2008 Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. Embo Reports. 9: 429-34. PMID 18451766 DOI: 10.1038/Embor.2008.56  1
2008 Lange V, Malmström JA, Didion J, King NL, Johansson BP, Schäfer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, Bühlmann P, Björck L, Domon B, Aebersold R. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Molecular & Cellular Proteomics : McP. 7: 1489-500. PMID 18408245 DOI: 10.1074/Mcp.M800032-Mcp200  1
2008 Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, et al. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature Biotechnology. 26: 305-12. PMID 18327244 DOI: 10.1038/Nbt1391  1
2008 Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, ... ... Deutsch EW, et al. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26: 164-7. PMID 18259167 DOI: 10.1038/Nbt0208-164  1
2008 Deutsch EW, Lam H, Aebersold R. Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiological Genomics. 33: 18-25. PMID 18212004 DOI: 10.1152/Physiolgenomics.00298.2007  1
2007 Pascal LE, Deutsch EW, Campbell DS, Korb M, True LD, Liu AY. The urologic epithelial stem cell database (UESC) - a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder. Bmc Urology. 7: 19. PMID 18072977 DOI: 10.1186/1471-2490-7-19  1
2007 Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H. Five years of progress in the standardization of proteomics data 4 th annual spring workshop of the HUPO-proteomics standards initiative - April 23-25, 2007. Ecole Nationale Supérieure (ENS), Lyon, France Proteomics. 7: 3436-3440. PMID 17907277 DOI: 10.1002/Pmic.200700658  1
2007 Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/Nbt1329  1
2007 Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, et al. A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology. 25: 576-83. PMID 17450130 DOI: 10.1038/Nbt1300  1
2007 Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. Development and validation of a spectral library searching method for peptide identification from MS/MS Proteomics. 7: 655-667. PMID 17295354 DOI: 10.1002/Pmic.200600625  1
2007 Chervitz SA, Parkinson H, Fostel JM, Causton HC, Sanson SA, Deutsch EW, Field D, Taylor CF, Rocca-Serra P, White J, Stoeckert CJ. Standards for functional genomics Bioinformatics: Tools and Applications. 293-329. DOI: 10.1007/978-0-387-92738-1_15  1
2006 King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biology. 7: R106. PMID 17101051 DOI: 10.1186/Gb-2006-7-11-R106  1
2006 Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, et al. Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Omics : a Journal of Integrative Biology. 10: 205-8. PMID 16901227 DOI: 10.1089/Omi.2006.10.205  1
2006 Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. Bmc Bioinformatics. 7: 286. PMID 16756676 DOI: 10.1186/1471-2105-7-286  1
2006 Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Research. 34: D655-8. PMID 16381952 DOI: 10.1093/Nar/Gkj040  1
2005 Chen SS, Deutsch EW, Yi EC, Li XJ, Goodlett DR, Aebersold R. Improving mass and liquid chromatography based identification of proteins using bayesian scoring. Journal of Proteome Research. 4: 2174-84. PMID 16335964 DOI: 10.1021/Pr050251C  1
2005 Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R. Human Plasma PeptideAtlas. Proteomics. 5: 3497-500. PMID 16052627 DOI: 10.1002/Pmic.200500160  1
2005 Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biology. 6: R9. PMID 15642101 DOI: 10.1186/Gb-2004-6-1-R9  1
2004 Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, et al. A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnology. 22: 1459-66. PMID 15529173 DOI: 10.1038/Nbt1031  1
2004 Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Research. 14: 2221-34. PMID 15520287 DOI: 10.1101/Gr.2700304  1
2004 Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biology. 5: R52. PMID 15287974 DOI: 10.1186/Gb-2004-5-8-R52  1
2004 Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, Fausto N, Katze MG, Aebersold R. A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Molecular & Cellular Proteomics : McP. 3: 1039-41. PMID 15269248 DOI: 10.1074/Mcp.D400001-Mcp200  1
2004 Deutsch EW, Korb H, True LD, Liu AY, Sorensen CM, Sherenz TM. 724: A Database Tool and Minimum Information Specification for Prostate and Bladder Experimental Data The Journal of Urology. 171: 192-192. DOI: 10.1016/S0022-5347(18)37973-4  1
2003 Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature Biotechnology. 21: 247-54. PMID 12610571 DOI: 10.1038/Nbt0303-247  1
2002 Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, ... ... Deutsch E, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology. 3: RESEARCH0046. PMID 12225585 DOI: 10.1186/Gb-2002-3-9-Research0046  1
2002 Margon B, Anderson SF, Harris HC, Strauss MA, Knapp GR, Fan X, Schneider DP, Vanden Berk DE, Schlegel DJ, Deutsch EW, Ivezić Z, Hall PB, Williams BF, Davidsen AF, Brinkmann J, et al. Faint high-latitude carbon stars discovered by the sloan digital sky survey: Methods and initial results Astronomical Journal. 124: 1651-1669. DOI: 10.1086/342284  1
2002 Callanan PJ, Curran P, Filippenko AV, Garcia MR, Margon B, Deutsch E, Anderson S, Homer L, Fender RP. The Peculiar Infrared Counterpart of GX 17+2 The Astrophysical Journal. 574. DOI: 10.1086/341880  1
2002 Homer L, Anderson SF, Margon B, Downes RA, Deutsch EW. Optical Identification of the X-Ray Burster X1746-370 in the Globular Cluster NGC 6441 The Astronomical Journal. 123: 3255-3262. DOI: 10.1086/340470  1
2001 Homer L, Deutsch EW, Anderson SF, Margon B. The Rapid Burster in Liller 1: The Chandra X-Ray Position and a Search for an Infrared Counterpart The Astronomical Journal. 122: 2627-2633. DOI: 10.1086/323545  1
2001 Homer L, Anderson SF, Margon B, Deutsch EW, Downes RA. Optical Identification of the X-Ray Burster in the Globular Cluster NGC 1851 The Astrophysical Journal. 550. DOI: 10.1086/319652  1
2000 Deutsch EW, Margon B, Anderson SF. Ultracompact X-Ray Binaries in Globular Clusters: Variability of the Optical Counterpart of X1832-330 in NGC 6652. The Astrophysical Journal. 530: L21-L24. PMID 10642196 DOI: 10.1086/312486  1
2000 Galama TJ, Tanvir N, Vreeswijk PM, Wijers RAMJ, Groot PJ, Rol E, van Paradijs J, Kouveliotou C, Fruchter AS, Masetti N, Pedersen H, Margon B, Deutsch EW, Metzger M, Armus L, et al. Evidence for a Supernova in Reanalyzed Optical and Near‐Infrared Images of GRB 970228 The Astrophysical Journal. 536: 185-194. DOI: 10.1086/308909  0.01
1999 Deutsch EW. The Optical Counterparts of the Luminous X‐Ray Binary Stars in Globular Clusters Publications of the Astronomical Society of the Pacific. 111: 916-916. DOI: 10.1086/316392  0.01
1999 Margon B, Deutsch EW. The Meinunger "Nicht Rote" Objects Publications of the Astronomical Society of the Pacific. 111: 45-49. DOI: 10.1086/316297  1
1999 Deutsch EW, Margon B, Anderson SF, Wachter S, Goss WM. Infrared Candidates for the Intense Galactic X-Ray Source GX 17+2 The Astrophysical Journal. 524: 406-413. DOI: 10.1086/307803  1
1999 Deutsch EW, Margon B, Anderson SF, Downes RA. Serendipitous Discovery of a Cataclysmic Variable in the Globular Cluster NGC 6624 The Astronomical Journal. 118: 2888-2893. DOI: 10.1086/301150  1
1999 Deutsch EW. Empirical uncertainty estimators for astrometry from digital databases The Astronomical Journal. 118: 1882-1887. DOI: 10.1086/301044  0.01
1998 Deutsch EW, Margon B, Bland‐Hawthorn J. A Technique for Narrowband Time Series Photometry: The X‐Ray Star V2116 Ophiuchi Publications of the Astronomical Society of the Pacific. 110: 912-916. DOI: 10.1086/316217  1
1998 Diercks A, Deutsch EW, Castander FJ, Corson C, Gilmore G, Lamb DQ, Tanvir N, Turner EL, Wyse R. The Optical Afterglow of GRB 971214: [ITAL]R[/ITAL] and [ITAL]J[/ITAL] Photometry The Astrophysical Journal. 503. DOI: 10.1086/311540  1
1998 Diercks A, Deutsch EW, Castander FJ, Corson C, Gilmore G, Lamb DQ, Tanvir N, Turner EL, Wyse R. The optical afterglow of GRB 971214: R and J photometry Astrophysical Journal. 503. DOI: 10.1086/311540  1
1998 Margon B, Deutsch EW. Complex Velocity Fields in the Shell of T Pyxidis The Astrophysical Journal. 498. DOI: 10.1086/311310  1
1998 Deutsch EW, Anderson SF, Margon B, Downes RA. The Probable Optical Counterpart of the Luminous X-Ray Source in NGC 6441* The Astrophysical Journal. 493: 775-780. DOI: 10.1086/305140  1
1998 Deutsch EW, Margon B, Anderson SF. A Search for the Optical Counterpart of the Luminous X-Ray Source in NGC 6652 The Astronomical Journal. 116: 1301-1307. DOI: 10.1086/300512  1
1997 Anderson SF, Margon B, Deutsch EW, Downes RA, Allen RG. Time-Resolved Ultraviolet Observations of the Globular Cluster X-Ray Source in NGC 6624: The Shortest Known Period Binary System* The Astrophysical Journal. 482. DOI: 10.1086/310672  1
1997 Margon B, Deutsch EW. Cc Bootis: Qso, Not Variable Halo Giant Publications of the Astronomical Society of the Pacific. 109: 673. DOI: 10.1086/133930  1
1996 Deutsch EW, Anderson SF, Margon B, Downes RA. An Ultraviolet-Excess Optical Candidate for the Luminous Globular Cluster X-Ray Source in NGC 1851 The Astrophysical Journal. 472. DOI: 10.1086/310373  1
1996 Deutsch EW, Margon B, Wachter S, Anderson SF. Hubble Space Telescope Imaging of Bright Galactic X-Ray Binaries in Crowded Fields The Astrophysical Journal. 471: 979-986. DOI: 10.1086/178025  1
1994 Deutsch EW. Positions and proper motions of dwarf carbon stars Publications of the Astronomical Society of the Pacific. 106: 1134. DOI: 10.1086/133489  0.01
1993 Bohlin RC, Deutsch EW, McQuade KA, Hill JK, Landsman WB, O'Connell RW, Roberts MS, Smith AM, Stecher TP. Ultraviolet Imaging Telescope: Globular Clusters in M31 The Astrophysical Journal. 417: 127-144. DOI: 10.1086/173297  0.01
1993 Deutsch EW, Allen RJ. The Structure of the Inner Eastern Spiral Arm of M83 The Astronomical Journal. 106: 1812-1818. DOI: 10.1086/116766  0.01
1993 Anderson SF, Margon B, Deutsch EW, Downes RA. Ultraviolet-excess selection of the counterpart to a globular cluster X-ray burster - Hubble Space Telescope images of the core of NGC 6712 The Astronomical Journal. 106: 1049-1054. DOI: 10.1086/116702  1
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