State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet
Open accessAbstract
The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected from many different laboratories, all reanalyzed through a uniform processing pipeline. The latest 2015-03 build contains substantially more input data than past releases, is mapped to a recent version of our merged reference proteome, and uses improved informatics processing and the development of the AtlasProphet to provide the highest quality results. Within the set of ∼20,000 neXtProt primary entries, 14,070 (70%) are confidently detected in the latest build, 5% are ambiguous, 9% are redundant, leaving the total percentage of proteins for which there are no mapping detections at just 16% (3166), all derived from over 133 million peptide-spectrum matches identifying more than 1 million distinct peptides using AtlasProphet to characterize and classify the protein matches. Improved handling for detection and presentation of single amino-acid variants (SAAVs) reveals the detection of 5326 uniquely mapping SAAVs across 2794 proteins. With such a large amount of data, the control of false positives is a challenge. We present the methodology and results for maintaining rigorous quality along with a discussion of the implications of the remaining sources of errors in the build.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The noncanonical MYBPC3 peptide had not been observed in PeptideAtlas or MassIVE-KB and had no identical match to any sequences of any taxonomy in RefSeq by BLASTP.
“The noncanonical peptide had not been observed in the peptide repositories PeptideAtlas (housing 1.4M peptides) (Deutsch et al., 2015) or MassIVE-KB (2.3 M peptides) (Wang et al., 2018a) and had no identical match to any sequences of any taxonomy in RefSeq by BLASTP (Boratyn et al., 2013).”
From Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome (2019) · cites this paper as Deutsch et al., 2015
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,535 · see citing works
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955 · see citing works
Keller, A., Nesvizhskii, A., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,970 · see citing works
A statistical model for identifying proteins by tandem mass spectrometry.
Nesvizhskii, A., Keller, A., Kolker, E., & Aebersold, R. (2003) · Analytical Chemistry · doi:10.1021/ac0341261 · Cited by 4,902 · see citing works
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Boeckmann, B. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg095 · Cited by 3,894 · see citing works
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
Vizcaíno, J. A., Deutsch, E. W., Wang, R., Csordás, A., Reisinger, F., Ríos, D., Dianes, J. A., Sun, Z., Farrah, T., Bandeira, N., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2839 · Cited by 2,735 · see citing works
Self-citationTANDEM: matching proteins with tandem mass spectra
Craig, R., & Beavis, R. C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth092 · Cited by 2,553 · see citing works
A draft map of the human proteome
Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198 · see citing works
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820 · see citing works
Activities at the Universal Protein Resource (UniProt)
The UniProt Consortium (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1140 · Cited by 1,736 · see citing works
Comet: An open‐source <scp>MS</scp> / <scp>MS</scp> sequence database search tool
Eng, J. K., Jahan, T. A., & Hoopmann, M. R. (2013) · PROTEOMICS · doi:10.1002/pmic.201200439 · Cited by 1,474 · see citing works
Proteogenomics: concepts, applications and computational strategies
Nesvizhskii, A. I. (2014) · Nature Methods · doi:10.1038/nmeth.3144 · Cited by 763 · see citing works
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R. (2009) · Cell · doi:10.1016/j.cell.2009.05.051 · Cited by 744 · see citing works
Open Source System for Analyzing, Validating, and Storing Protein Identification Data
Craig, R., Cortens, J. P., & Beavis, R. C. (2004) · Journal of Proteome Research · doi:10.1021/pr049882h · Cited by 696 · see citing works
The International Protein Index: An integrated database for proteomics experiments
Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., & Apweiler, R. (2004) · PROTEOMICS · doi:10.1002/pmic.200300721 · Cited by 693 · see citing works
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Keller, A., Eng, J. K., Zhang, N., Li, X., & Aebersold, R. H. (2005) · Molecular Systems Biology · doi:10.1038/msb4100024 · Cited by 692 · see citing works
Shteynberg, D. D., Deutsch, E. W., Lam, H., Eng, J. K., Sun, Z., Tasman, N., Mendoza, L., Moritz, R. L., Aebersold, R. H., & Nesvizhskii, A. I. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.007690 · Cited by 548 · see citing works
Self-citationPeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
Deutsch, E. W., Lam, H., & Aebersold, R. H. (2008) · EMBO Reports · doi:10.1038/embor.2008.56 · Cited by 541 · see citing works
Self-citationIMGT®, the international ImMunoGeneTics information system®
Lefranc, M., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G., Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J., et al. (2004) · Nucleic Acids Res. · doi:10.1093/nar/gkn838 · Cited by 521 · see citing works
A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas
Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S., Sun, Z., Bletz, J., Mallick, P., Katz, J. E., Malmström, J. A., Ossola, R., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.006353 · Cited by 446 · see citing works
Self-citationA Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets
Savitski, M. M., Wilhelm, M., Hahne, H., Küster, B., & Bantscheff, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.046995 · Cited by 436 · see citing works
The human proteome project: current state and future direction
Legrain, P., Aebersold, R., Archakov, A., Bairoch, A., Bala, K., Beretta, L., Bergeron, J., Borchers, C. H., Corthals, G. L., Costello, C. E., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.009993 · Cited by 352 · see citing works
Self-citationDeutsch, E. W., Mendoza, L., Shteynberg, D., Slagel, J., Sun, Z., & Moritz, R. L. (2015) · PROTEOMICS – Clinical Applications · doi:10.1002/prca.201400164 · Cited by 342 · see citing works
Self-citationReiter, L., Claassen, M., Schrimpf, S. P., Jovanovic, M., Schmidt, A., Buhmann, J. M., Hengartner, M. O., & Aebersold, R. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900317-mcp200 · Cited by 312 · see citing works
Ellis, M. J., Gillette, M. A., Carr, S. A., Paulovich, A. G., Smith, R. D., Rodland, K., Townsend, R. R., Kinsinger, C. R., Mesri, M., Rodriguez, H., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0219 · Cited by 311 · see citing works
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
Desiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P., King, N. L., Eng, J. K., Aderem, A. A., Boyle, R., Brunner, E., Donohoe, S., et al. (2004) · Genome biology · doi:10.1186/gb-2004-6-1-r9 · Cited by 293 · see citing works
Self-citationKaviar: an accessible system for testing SNV novelty
Glusman, G., Caballero-Pérez, J., Mauldin, D. E., Hood, L., & Roach, J. C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr540 · Cited by 219 · see citing works
MacLean, B., Eng, J. K., Beavis, R. C., & McIntosh, M. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl379 · Cited by 210 · see citing works
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
Deutsch, E. W., Lam, H., & Aebersold, R. H. (2008) · Physiological Genomics · doi:10.1152/physiolgenomics.00298.2007 · Cited by 154 · see citing works
Self-citationFarrah, T., Deutsch, E. W., Omenn, G. S., Sun, Z., Watts, J. D., Yamamoto, T., Shteynberg, D. D., Harris, M., & Moritz, R. L. (2013) · Journal of Proteome Research · doi:10.1021/pr4010037 · Cited by 132 · see citing works
Self-citationMetrics for the Human Proteome Project 2013–2014 and Strategies for Finding Missing Proteins
Lane, L., Bairoch, A., Beavis, R. C., Deutsch, E. W., Gaudet, P., Lundberg, E., & Omenn, G. S. (2014) · Journal of Proteome Research · doi:10.1021/pr401144x · Cited by 129 · see citing works
Self-citationneXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects
Gaudet, P., Argoud-Puy, G., Cusin, I., Duek, P., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Zahn-Zabal, M., Zwahlen, C., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr300830v · Cited by 124 · see citing works
The State of the Human Proteome in 2012 as Viewed through PeptideAtlas
Farrah, T., Deutsch, E. W., Hoopmann, M. R., Hallows, J. L., Sun, Z., Huang, C., & Moritz, R. L. (2012) · Journal of Proteome Research · doi:10.1021/pr301012j · Cited by 120 · see citing works
Self-citationConfetti: A Multiprotease Map of the HeLa Proteome for Comprehensive Proteomics
Guo, X., Trudgian, D. C., Lemoff, A. S., Yadavalli, S., & Mirzaei, H. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.035170 · Cited by 103 · see citing works
Analyzing the First Drafts of the Human Proteome
Ezkurdia, I., Vázquez, J., Valencia, A., & Tress, M. L. (2014) · Journal of Proteome Research · doi:10.1021/pr500572z · Cited by 102 · see citing works
Kusebauch, U., Deutsch, E. W., Campbell, D. S., Sun, Z., Farrah, T., & Moritz, R. L. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1325s46 · Cited by 64 · see citing works
Self-citationA B ovine P eptide A tlas of milk and mammary gland proteomes
Bislev, S. L., Deutsch, E. W., Sun, Z., Farrah, T., Aebersold, R. H., Moritz, R. L., Bendixen, E., & Codrea, M. C. (2012) · PROTEOMICS · doi:10.1002/pmic.201200057 · Cited by 40 · see citing works
Self-citationShanmugam, A. K., Yocum, A. K., & Nesvizhskii, A. I. (2014) · Journal of Proteome Research · doi:10.1021/pr500496p · Cited by 29 · see citing works
The Equine PeptideAtlas: A resource for developing proteomics‐based veterinary research
Bundgaard, L., Jacobsen, S. E., Sørensen, M. A., Sun, Z., Deutsch, E. W., Moritz, R. L., & Bendixen, E. (2014) · PROTEOMICS · doi:10.1002/pmic.201300398 · Cited by 22 · see citing works
Self-citationA Candida albicans PeptideAtlas
Vialás, V., Sun, Z., y Penha, C. V. L., Carrascal, M., Abián, J., Monteoliva, L., Deutsch, E. W., Aebersold, R. H., Moritz, R. L., & Gil, C. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.06.020 · Cited by 21 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
UniProt: the universal protein knowledgebase
The UniProt Consortium (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1099 · Cited by 4,436 · see citing works
“We have developed a pipeline that provides evidence annotations to UniProtKB records using proteomics datasets currently from PeptideAtlas (21) MaxQB (22) and Encyclopedia of Proteome Dynamics (23).”
MethodAlternative Splicing May Not Be the Key to Proteome Complexity
Tress, M. L., Abascal, F., & Valencia, A. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.08.008 · Cited by 341 · see citing works
“Combining many sources of data comes at a cost [26,35], so it is vital to control false-positive rates.”
BackgroundHuman SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Kusebauch, U., Campbell, D. S., Deutsch, E. W., Chu, C. S., Spicer, D. A., Brusniak, M.-Y., Slagel, J., Sun, Z., Stevens, J., Grimes, B., et al. (2016) · Cell · doi:10.1016/j.cell.2016.06.041 · Cited by 310 · see citing works
“The state of the human proteome as viewed through PeptideAtlas in 2015 (Deutsch et al., 2015b), which incorporates data from large-scale proteomic measurements, reports 133 million high-quality PSMs, identifying more than 1 million distinct peptides that collectively represent 14,070 (70%) confidently identified human…”
Self-citationHoofnagle, A. N., Whiteaker, J. R., Carr, S. A., Kuhn, E. W., Liu, T., Massoni, S. A., Thomas, S. N., Townsend, R. R., Zimmerman, L. J., Boja, E. S., et al. (2015) · Clinical Chemistry · doi:10.1373/clinchem.2015.250563 · Cited by 230 · see citing works
“GPM (23), PRIDE (24), Peptide Atlas (25-27), PhosphoSitePlus (28)].”
BackgroundSelf-citationSchwenk, J. M., Omenn, G. S., Sun, Z., Campbell, D. S., Baker, M. S., Overall, C. M., Aebersold, R. H., Moritz, R. L., & Deutsch, E. W. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00467 · Cited by 223 · see citing works
“In order to gain a historical perspective on the total number of proteins gained for each of our consecutive builds in a consistent manner, we have remapped all the peptides from these builds to the 2017-01 version of neXtProt using the AtlasProphet algorithm (23).”
MethodSelf-citationAccessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)Preprint
Rangwala, S. H., Kuznetsov, A., Ananiev, V., Asztalos, A., Borodin, E. A., Evgeniev, V. I., Joukov, V., Lotov, V., Pannu, R., Rudnev, D., et al. (2020) · Genome Research · doi:10.1101/gr.266932.120 · Cited by 222 · see citing works
“2015) Polyadenylation sites RNA-seq exon coverage and intron-spanning reads and features (NCBI-specific analysis) Peptides from PeptideAtlas (Deutsch et al. 2015) GWIPS ribosome profiling (Michel et al.”
MethodA high-stringency blueprint of the human proteome
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210 · see citing works
Self-citationThe neXtProt knowledgebase in 2020: data, tools and usability improvements
Zahn‐Zabal, M., Michel, P.-A., Gateau, A., Nikitin, F., Schaeffer, M., Audot, E., Gaudet, P., Duek, P. D., Teixeira, D., de Laval, V. R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz995 · Cited by 215 · see citing works
“The data from UniProtKB (2) is currently supplemented with data from Bgee (8), HPA (5,9), PeptideAtlas (10), SRMAtlas (11), GOA (12), dbSNP (13), Ensembl (14), COSMIC (15), DKF GFP-cDNA localization (16,17), Weizmann Institute of Science’s Kahn Dynamic Proteomics Database (18), IntAct (19), GlyConnect (20), gnomAD (6)…”
MethodAn update on sORFs.org: a repository of small ORFs identified by ribosome profiling
Olexiouk, V., Criekinge, W. V., & Menschaert, G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1130 · Cited by 194 · see citing works
“To build in a second layer of translational evidence based on MS, integration of sORFs.org with PeptideAtlas (41) and NextProt (42) is investigated.”
BackgroundThe neXtProt knowledgebase on human proteins: 2017 update
Gaudet, P., Michel, P.-A., Zahn-Zabal, M., Britan, A., Cusin, I., Domagalski, M., Duek, P. D., Gateau, A., Gleizes, A., Hinard, V., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1062 · Cited by 164 · see citing works
“The authors thank the PeptideAtlas team for fruitful exchanges regarding proteomics data handling.”
BackgroundInfluentialHuman Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1
Deutsch, E. W., Overall, C. M., Eyk, J. E. V., Baker, M. S., Paik, Y., Weintraub, S. T., Lane, L., Martens, L., Vandenbrouck, Y., Kusebauch, U., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00392 · Cited by 166 · see citing works
“At that time, this was only PRIDE 20–22 for shotgun data, and PASSEL 23 , a part of PeptideAtlas 24–26 , for SRM data.”
Self-citationInference and quantification of peptidoforms in large sample cohorts by SWATH-MS
Rosenberger, G., Liu, Y., Röst, H. L., Ludwig, C., Buil, A., Bensimon, A., Soste, M., Spector, T. D., Dermitzakis, E. T., Collins, B. C., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3908 · Cited by 121 · see citing works
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Deutsch, E. W., Lane, L., Overall, C. M., Bandeira, N., Baker, M. S., Pineau, C., Moritz, R. L., Corrales, F., Orchard, S., Van Eyk, J. E., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00542 · Cited by 122 · see citing works
Self-citationQuantifying the impact of public omics data
Pérez‐Riverol, Y., Zorin, A., Dass, G., Vu, M.-T., Xu, P., Glont, M., Vizcaíno, J. A., Jarnuczak, A. F., Petryszak, R., Ping, P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11461-w · Cited by 109 · see citing works
Gillespie, M. A., Palii, C. G., Sanchez-Taltavull, D., Shannon, P., Longabaugh, W. J. R., Downes, D. J., Sivaraman, K., Espinoza, H. M., Hughes, J. R., Price, N. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.031 · Cited by 110 · see citing works
Accelerating the search for the missing proteins in the human proteome
Baker, M. S., Ahn, S. B., Mohamedali, A., Islam, M. T., Cantor, D., Verhaert, P. D., Fanayan, S., Sharma, S., Nice, E. C., Connor, M., et al. (2017) · Nature Communications · doi:10.1038/ncomms14271 · Cited by 100 · see citing works
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
Deutsch, E., Orchard, S., Binz, P., Bittremieux, W., Eisenacher, M., Hermjakob, H., Kawano, S., Lam, H. H. N., Mayer, G., Menschaert, G., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00370 · Cited by 88 · see citing works
Self-citationOmenn, G. S., Lane, L., Lundberg, E. K., Beavis, R. C., Nesvizhskii, A. I., & Deutsch, E. W. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00499 · Cited by 93 · see citing works
Self-citationExpanding the human proteome with microproteins and peptideins
Deutsch, E. W., Kok, L. W., Mudge, J. M., Valls, C., Jungreis, I., Ruiz‐Orera, J., Sun, Z., Kusebauch, U., Fierro-Monti, I., Abelin, J. G., et al. (2026) · Nature · doi:10.1038/s41586-026-10459-x · Cited by 91 · see citing works
“…using the Trans-Proteomic Pipeline (TPP) 53,54 v.7.0 tools Peptide-Prophet 55 , iProphet 56 and PTMProphet 57 , and the results were mapped to the human proteome using ProteoMapper 58 , taking known variants into account, and to the genome using the ENSEMBL 59 toolkit as previously described 60 .”
InfluentialSelf-citationSplice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Lau, E., Han, Y., Williams, D. R., Thomas, C. T., Shrestha, R., Wu, J. C., & Lam, M. P. Y. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.026 · Cited by 67 · see citing works
“The noncanonical peptide had not been observed in the peptide repositories PeptideAtlas (housing 1.4M peptides) (Deutsch et al., 2015) or MassIVE-KB (2.3 M peptides) (Wang et al., 2018a) and had no identical match to any sequences of any taxonomy in RefSeq by BLASTP (Boratyn et al., 2013).”
BackgroundInfluentialParker, G. J., McKiernan, H. E., Legg, K. M., & Goecker, Z. C. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102529 · Cited by 78 · see citing works
Omenn, G. S., Lane, L., Lundberg, E. K., Beavis, R. C., Overall, C. M., & Deutsch, E. W. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00511 · Cited by 77 · see citing works
Self-citationEvolution and implications of de novo genes in humans
Broeils, L. A., Ruiz‐Orera, J., Snel, ., Hübner, N., & van Heesch, S. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02014-y · Cited by 76 · see citing works
Guo, Z., Zhang, Y., Zou, L., Wang, D., Shao, C., Wang, Y., Sun, W., & Zhang, L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0133270 · Cited by 70 · see citing works
Kulyyassov, A., Fresnais, M., & Longuespée, R. (2021) · PROTEOMICS · doi:10.1002/pmic.202100153 · Cited by 65 · see citing works
“Other databases can also contain large amounts of data from MRM experiments and help choosing the right candidate peptides or transitions and support MRM/PRM method development: (i) PeptideAtlas [97], a collection of peptides identified from MS/MS proteomic experiments, and the related (ii) SRMAtlas [98], a collection…”
BackgroundGlusman, G., Rose, P. W., Prlić, A., Dougherty, J. G., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T. R., Bock, C., et al. (2017) · Genome Medicine · doi:10.1186/s13073-017-0509-y · Cited by 60 · see citing works
“mass spectrometry [56, 57], so that the variations in the latter resources can be depicted using the tools in MuPIT.”
MethodSelf-citationThe 2022 Report on the Human Proteome from the HUPO Human Proteome Project
Omenn, G. S., Lane, L., Overall, C. M., Pineau, C., Packer, N. H., Cristea, I. M., Lindskog, C., Weintraub, S. T., Orchard, S. E., Roehrl, M. H. A., et al. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00498 · Cited by 60 · see citing works
Self-citationProgress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project
Omenn, G. S., Lane, L., Lundberg, E. K., Overall, C. M., & Deutsch, E. W. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00375 · Cited by 55 · see citing works
Self-citationExpanding the Use of Spectral Libraries in Proteomics
Deutsch, E. W., Pérez‐Riverol, Y., Chalkley, R. J., Wilhelm, M., Tate, S. A., Sachsenberg, T. T., Walzer, M., Käll, L., Delanghe, B., Böcker, S., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00485 · Cited by 54 · see citing works
Self-citationPark, G. W., Hwang, H., Kim, K. H., Lee, J. Y., Lee, H. K., Park, J. Y., Ji, E. S., Park, S. K. R., Yates, J. R., Kwon, K., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00376 · Cited by 47 · see citing works
Excitonic states and structural stability in two-dimensional hybrid organic-inorganic perovskites
Lekina, Y., & Shen, Z. (2019) · Journal of Science Advanced Materials and Devices · doi:10.1016/j.jsamd.2019.03.005 · Cited by 49 · see citing works
Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins
Zhang, Y., Li, Q., Wu, F., Zhou, R., Qi, Y., Su, N., Chen, L., Xu, S., Jiang, T., Zhang, C., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00435 · Cited by 47 · see citing works
Eckhard, U., Marino, G., Abbey, S. R., Tharmarajah, G., Matthew, I., & Overall, C. M. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00579 · Cited by 46 · see citing works
Omenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y.-K., Van Eyk, J. E., Liu, S., Pennington, S., Snyder, M. P., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00434 · Cited by 40 · see citing works
Self-citationI'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets
Chard, K., D’Arcy, M., Heavner, B., Foster, I. T., Kesselman, C., Madduri, R., Rodriguez, A., Soiland‐Reyes, S., Goble, C., Clark, K. A., et al. (2016) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata.2016.7840618 · Cited by 43 · see citing works
Self-citationOmenn, G. S., Lane, L., Overall, C. M., Cristea, I. M., Corrales, F. J., Lindskog, C., Paik, Y., Eyk, J. E. V., Liu, S., Pennington, S. R., et al. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00485 · Cited by 41 · see citing works
Self-citationOmenn, G. S., Lane, L., Overall, C. M., Paik, Y., Cristea, I. M., Corrales, F. J., Lindskog, C., Weintraub, S. T., Roehrl, M. H. A., Liu, S., et al. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00590 · Cited by 39 · see citing works
Self-citationGuo, J., Cui, Y., Yan, Z., Luo, Y., Zhang, W., Deng, S., Tang, S., Zhang, G., He, Q., & Wang, T. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00391 · Cited by 37 · see citing works
Kitata, R. B., Dimayacyac-Esleta, B. R. T., Choong, W.-K., Tsai, C.-F., Lin, T., Tsou, C., Weng, S.-H., Chen, Y., Yang, P.-C., Arco, S. D., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00477 · Cited by 32 · see citing works
Lee, H., & Kim, S. I. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042187 · Cited by 31 · see citing works
The potential clinical impact of the release of two drafts of the human proteome
Ezkurdia, I., Calvo, E., del Pozo, Á., Vázquez, J., Valencia, A., & Tress, M. L. (2015) · Expert Review of Proteomics · doi:10.1586/14789450.2015.1103186 · Cited by 26 · see citing works
“Largescale proteomics studies also have a role to play in identifying common single amino acid variants and minor annotation errors, [18] while we have shown that proteomics can help determine the dominant cellular isoform for many genes.”
BackgroundMethodInfluentialEngineered SH2 Domains for Targeted Phosphoproteomics
Martyn, G. D., Veggiani, G., Kusebauch, U., Morrone, S. R., Yates, B. P., Singer, A. U., Tong, J., Manczyk, N., Gish, G. D., Sun, Z., et al. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.2c00051 · Cited by 26 · see citing works
Self-citationFlexible and Fast Mapping of Peptides to a Proteome with ProteoMapper
Mendoza, L., Deutsch, E., Sun, Z., Campbell, D., Shteynberg, D. D., & Moritz, R. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00544 · Cited by 21 · see citing works
Self-citationUnderstanding missing proteins: a functional perspective
Zhou, L., Wong, L., & Goh, W. W. B. (2017) · Drug Discovery Today · doi:10.1016/j.drudis.2017.11.011 · Cited by 21 · see citing works
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community
Nissa, M. U., Reddy, P. J., Pinto, N., Sun, Z., Ghosh, B., Moritz, R. L., Goswami, M., & Srivastava, S. (2022) · Scientific Data · doi:10.1038/s41597-022-01259-9 · Cited by 21 · see citing works
Self-citationEnhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
Guruceaga, E., Garín-Muga, A., Prieto, G., Bejarano, B., Marcilla, M., Marín‐Vicente, C., Pérez‐Riverol, Y., Casal, J. I., Vizcaíno, J. A., Corrales, F. J., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00388 · Cited by 18 · see citing works
Clinical implications of recent advances in proteogenomics
Locard‐Paulet, M., Pible, O., de Peredo, A. G., Alpha‐Bazin, B., Almunia, C., Burlet‐Schiltz, O., & Armengaud, J. (2015) · Expert Review of Proteomics · doi:10.1586/14789450.2016.1132169 · Cited by 17 · see citing works
Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light
Paik, Y., Omenn, G. S., Overall, C. M., Deutsch, E. W., & Hancock, W. S. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00785 · Cited by 15 · see citing works
Self-citationMetaPep: A core peptide database for faster human gut metaproteomics database searches
Sun, Z., Ning, Z., Cheng, K., Duan, H., Wu, Q., Mayne, J., & Figeys, D. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.08.025 · Cited by 14 · see citing works
“When necessary, MetaPep is able to append peptide sequences and spectra in the available human spectral libraries from PeptideAtlas [36] or NIST [37].”
BackgroundSelf-citationTholey, A., Taylor, N. L., Heazlewood, J. L., & Bendixen, E. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00408 · Cited by 13 · see citing works
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization
Paul, P., Antonydhason, V., Gopal, J., Haga, S. W., Hasan, N., & Oh, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21030961 · Cited by 13 · see citing works
Musiani, D., Massignani, E., Cuomo, A., Yadav, A., & Bonaldi, T. (2020) · Current Protein and Peptide Science · doi:10.2174/1389203721666200426232531 · Cited by 12 · see citing works
Myllykoski, M., Sutinen, A., Koski, M. K., Kallio, J. P., Raasakka, A., Myllyharju, J., Wierenga, R. K., & Koivunen, P. (2021) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.016542 · Cited by 12 · see citing works
Hwang, H., Park, G. W., Park, J. Y., Lee, H. K., Lee, J. Y., Jeong, J. E., Park, S. K. R., Yates, J. R., Kwon, K., Park, Y. M., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00223 · Cited by 11 · see citing works
Devising a Consensus Framework for Validation of Novel Human Coding Loci
Bruford, E. A., Lane, L., & Harrow, J. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00688 · Cited by 10 · see citing works
An Efficient Faiss-Based Search Method for Mass Spectral Library Searching
Qin, C., Deng, C., Huang, J., Shu, K., & Bai, M. (2020) · International Conference on Advanced Electronic Materials, Computers and Software Engineering (AEMCSE) · doi:10.1109/aemcse50948.2020.00116 · Cited by 9 · see citing works
Proteogenomic Tools and Approaches to Explore Protein Coding Landscapes of Eukaryotic Genomes
Kumar, D., & Dash, D. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-42316-6_1 · Cited by 9 · see citing works
Cho, J.-Y., Lee, H., Jeong, S.-K., & Paik, Y. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b01019 · Cited by 9 · see citing works
Worming into the Uncharacterized Human Proteome
Duek, P. D., & Lane, L. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00435 · Cited by 9 · see citing works
A tool for integrating genetic and mass spectrometry‐based peptide data: Proteogenomics Viewer
Kroll, J. E., da Silva, V. L., SOUZA, S. J. D., & de Souza, G. A. (2017) · BioEssays · doi:10.1002/bies.201700015 · Cited by 9 · see citing works
“Arguably, one of the best and most complete MS2 peptide identification repositories is the PeptideAtlas Project [16, 17], which catalog and report identified peptides from thousands of publications and is often reviewed and updated.”
BackgroundA comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage
Vialás, V., Sun, Z., Reales‐Calderón, J. A., Hernáez, M. L., Casas, V., Carrascal, M., Abián, J., Monteoliva, L., Deutsch, E. W., Moritz, R. L., et al. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.10.019 · Cited by 8 · see citing works
Self-citationJeong, S.-K., Hancock, W. S., & Paik, Y. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00541 · Cited by 8 · see citing works
What will neXtProt help us achieve in 2020 and beyond?
Zahn‐Zabal, M., & Lane, L. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1733418 · Cited by 7 · see citing works
Mosna, S., & Dormann, D. (2025) · BioEssays · doi:10.1002/bies.70084 · Cited by 6 · see citing works
Prediction of Protein-Protein Interactions: Looking Through the Kaleidoscope
Laddach, A., Chung, S. S., & Fraternali, F. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20470-6 · Cited by 6 · see citing works
UNIPROT DATABASE - UNIVERSAL INFORMATION RESOURCE OF PROTEIN SEQUENCES
Kulyyassov, A. (2022) · Eurasian journal of applied biotechnology · doi:10.11134/btp.1.2022.1 · Cited by 5 · see citing works
Steadman, K., You, S., Srinivas, D., Mouakkad, L., Yan, Y., Kim, M., Venugopal, S. V., Tanaka, H., & Freeman, M. R. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1206259 · Cited by 5 · see citing works
“, 2017) and eight potential frames were identified, but these possible peptide sequences could not be identified in human proteomic data using the peptide atlas (Desiere et al., 2006; Deutsch et al., 2015).”
BackgroundHwang, H., Park, G. W., Kim, K. H., Lee, J. Y., Lee, H. K., Ji, E. S., Park, S. K. R., Xu, T., Yates, J. R., Kwon, K., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00472 · Cited by 5 · see citing works
Islam, M. T., Mohamedali, A., Ahn, S. B., Nawar, I., Baker, M. S., & Ranganathan, S. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6740-7_13 · Cited by 5 · see citing works
Jabeen, A., Mohamedali, A., & Ranganathan, S. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20167-2 · Cited by 4 · see citing works
Lih, T. M., Choong, W.-K., Chen, Y., & Sung, T. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00052 · Cited by 4 · see citing works
Myllykoski, M., Sutinen, A., Koski, M. K., Kallio, J. P., Raasakka, A., Myllyharju, J., Wierenga, R. K., & Koivunen, P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.25.354423 · Cited by 3 · see citing works
“However, there is no published evidence of this isoform appears in protein form and there are no peptides listed in PeptideAtlas (26) that correspond to the 61 residues unique for this isoform.”
BackgroundA cell type-resolved proteomic atlas of the human bodyPreprint
Weiss, C. A. M., Sjöstedt, E., Debnath, A., Ben‐Moshe, S., Diedrich, L., Zwahlen, M., Oeller, M., Wahle, M., Skarwan, E., Heymann, T., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.26.727663 · Cited by 4 · see citing works
Evaluation of PE5 Entries on the Human Proteome Project Target List
Zheng, C., Andken, M., Mudge, J. M., Magrane, M., Orchard, S., Sun, Z., & Deutsch, E. W. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00167 · Cited by 1 · see citing works
Self-citationGuo, Z., Zhang, Y., Zou, L., Wang, D., Shao, C., Wang, Y., Sun, W., & Zhang, L. (2019) · PLoS ONE · doi:10.1371/journal.pone.0213213 · Cited by 1 · see citing works
Nissa, M. U., Reddy, J. S., Mukherjee, A., Pinto, N., Ghosh, B., Sun, Z., Ghantasala, S., Chetanya, C., Shenoy, S. V., George, T., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-397364/v1
Self-citationMultiomics data analysis identifies TM4SF4 as a cell surface target in hepatocellular carcinomaPreprint
Wong, K. K., & Hamid, S. S. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.01.601537
Multiomics in silico analysis identifies TM4SF4 as a cell surface target in hepatocellular carcinoma
Wong, K. K., & Hamid, S. S. A. (2025) · PLoS ONE · doi:10.1371/journal.pone.0307048
Jácome, A. S. V. (2016) · theses.fr (ABES) · doi:10.70675/f5b9ae4fz21ffz4c4azbe12zca5959d63295
“Data provided by the scientific community in databases or repositories (SRMAtlas [160], PeptideAtlas [161], ProteomeXchange [162], ProteomicsDB [163]).”
BackgroundFerreira, R. M. S., Amado, F. M., & Vitorino, R. M. P. (2026) · Expert Review of Proteomics · doi:10.1080/14789450.2026.2738952
“PeptideAtlas provides a complementary model: heterogeneous datasets from many laboratories are reanalyzed through a uniform processing pipeline and confidence framework, turning independent experiments into a comparable evidence resource [121].”
FAIRsharing record for: Human Proteome Project Mass Spectrometry Data Interpretation Guidelines
FAIRsharing Team, & Anderson, L. (2024) · FAIRsharing.org · doi:10.25504/fairsharing.9b1474
FAIRsharing record for: neXtProt
FAIRsharing Team (2015) · FAIRsharing.org · doi:10.25504/fairsharing.62evqh
FAIRsharing record for: NCBI Genome Data Viewer
FAIRsharing Team, & Lister, A. (2022) · FAIRsharing.org · doi:10.25504/fairsharing.b05f99
- Authors
- Deutsch, E. W., Sun, Z., Campbell, D., Kusebauch, U., Chu, C. S., Mendoza, L., Shteynberg, D., Omenn, G. S., & Moritz, R. L.
- Affiliations
- Institute for Systems Biology (US)
- University of Michigan (US)
- Corresponding author
- Deutsch, Eric W.
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-07-24
- Volume
- 14
- Issue
- 9
- Pages
- 3461-3473
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC4755269
- OpenAlex
- W2409617262
- Cited by
- 80
- References
- 40
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 1 · 2023: 3 · 2022: 5 · 2021: 5 · 2020: 9 · 2019: 9 · 2018: 3 · 2017: 14 · 2016: 12 · 2015: 13
- FWCI
- 6.38
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (0923536)
- Seventh Framework Programme (260558)
- National Institute of Environmental Health Sciences (U54ES017885)
- National Institute of General Medical Sciences (2P50GM076547, R01GM087221)
- National Human Genome Research Institute (RC2HG005805)
- National Institute of Biomedical Imaging and Bioengineering (U54EB020406)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- human proteome, peptide identification, peptide-spectrum matches, single amino acid variants, false positive control
- MeSH terms
- Amino Acid Sequence, Humans, Molecular Sequence Data, Proteins, Sequence Homology, Amino Acid, Amino Acid Substitution, Databases, Protein, Proteomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
