YPED: An integrated bioinformatics suite and database for mass spectrometry-based proteomics research

Genomics, Proteomics and Bioinformatics

Volumn 13, Issue 1, 2015, Pages 25-35

  Colangelo, Christopher M ^a,b   Shifman, Mark ^a   Cheung, Kei Hoi ^a,c   Stone, Kathryn L ^a,b   Carriero, Nicholas J ^a,d   Gulcicek, Erol E ^a,b   Lam, TuKiet T ^a,b   Wu, Terence ^a,b   Bjornson, Robert D ^a,d   Bruce, Can ^a,b   Nairn, Angus C ^a   Rinehart, Jesse ^a,b   Miller, Perry L ^a,c   Williams, Kenneth R ^a,b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

^c VA CONNECTICUT HEALTHCARE SYSTEM   (United States)

^d Yale University   (United States)

Author keywords

Bioinformatics; Database; Mass spectrometry; Proteomics; Repository; Spectral library

Indexed keywords

PEPTIDE; PHOSPHOPEPTIDE; PROTEIN; PEPTIDE FRAGMENT; PROTEOME;

ARTICLE; AUTOMATION; BIOINFORMATICS; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; LABORATORY; LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY; MASS SPECTROMETRY; MEDICAL RESEARCH; MONITORING; MULTIPLE REACTION MONITORING; PEPTIDE LIBRARY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN LOCALIZATION; PROTEOMICS; QUANTITATIVE ANALYSIS; SCORING SYSTEM; SELECTIVE REACTION MONITORING; TANDEM MASS SPECTROMETRY; YALE PROTEIN EXPRESSION DATABASE; BIOLOGY; HUMAN; LIQUID CHROMATOGRAPHY; PROCEDURES;

CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; PEPTIDE FRAGMENTS; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84925632988     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2014.11.002     Document Type: Article

References (40)

1. Kenyon G., DeMarini D., Fuchs E., Galas D.J., Kirsch J., Leyh T., et al. Defining the mandate of proteomics in the post-genomics era: workshop report. Mol Cell Proteomics 2002, 10:763-780.
2. Editorial. Democratizing proteomics data. Nat Biotechnol 2007;25:26.
3. Vizcaíno J., Foster J., Martens L. Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J Proteomics 2010, 73:2136-2146.
4. Craig R., Cortens J., Beavis R. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 2004, 3:1234-1242.
5. Martens L., Hermjakob H., Jones P., Adamski M., Taylor C., States D., et al. PRIDE: the proteomics identifications database. Proteomics 2005, 5:3537-3545.
6. Deutsch W., Lam H., Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 2008, 9:429-434.
7. Kolker E., Higdon R., Haynes W., Welch D., Broomall W., Lancet D., et al. MOPED: Model Organism Protein Expression Database. Nucleic Acids Res 2012, 40:D1093-D1099.
8. Nanjappa V., Thomas J.K., Marimuthu A., Muthusamy B., Radhakrishnan A., Sharma R., et al. Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Res 2014, 42:D959-D965.
9. Editorial. Thou shalt share your data. Nat Methods 2008;5:209.
10. Orchard S., Hermjakob H., Julian R., Runte K., Sherman D., Wojcik J., et al. Common interchange standards for proteomics data: public availability of tools and schema. Proteomics 2004, 4:490-491.
11. Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K., Jones A.R., et al. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 2007, 25:887-893.
12. Schaab C., Geiger T., Stoehr G., Cox J., Mann M. Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol Cell Proteomics 2012, 11. M111.014068.
13. Shifman M., Li Y., Colangelo C., KS KL, Wu T., Cheung K., et al. YPED: a web-accessible database system for protein expression analysis. J Proteome Res 2007, 6:4019-4024.
14. Sharma V., Eckels J., Taylor G.K., Shulman N.J., Stergachis A.B., Joyner S.A., et al. Panorama: a targeted proteomics knowledge base. J Proteome Res 2014, 13:4205-4210.
15. Huttenhain R., Malmstrom J., Picotti P., Aebersold R. Perspectives of targeted mass spectrometry for protein biomarker verification. Curr Opin Chem Biol 2009, 13:518-525.
16. Picotti P., Lam H., Campbell D., Deutsch E., Mirzaei H., Ranish J., et al. A database of mass spectrometric assays for the yeast proteome. Nat Methods 2008, 5:913-914.
17. Farrah T., Deutsch E., Kreisberg R., Sun Z., Campbell D., Mendoza L., et al. PASSEL: the PeptideAtlas SRMexperiment library. Proteomics 2012, 12:1170-1175.
18. Kim M.S., Pinto S.M., Getnet D., Nirujogi R.S., Manda S.S., Chaerkady R., et al. A draft map of the human proteome. Nature 2014, 509:575-581.
19. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
20. Unlü M., Morgan M., Minden J. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18:2071-2077.
21. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
22. Ross P., Huang Y., Marchese J., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
23. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
24. Ong S., Blagoev B., Kratchmarova I., Kristensen D., Steen H., Pandey A., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-378.
25. Asara J., Christofk H., Freimark L., Cantley L. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 2008, 8:994-999.
26. Savitsk M., Lemeer S., Boesche M., Lang M., Mathieson T., Bantscheff M., et al. Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 2011, 10. M110.003830.
27. Taus T., Köcher T., Pichler P., Paschke C., Schmidt A., Henrich C., et al. Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 2011, 10:5354-5362.
28. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
29. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res 1994, 22:3578-3580.
30. Ishihama Y., Oda Y., Tabata T., Sato T., Nagasu T., Rappsilber J., et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
31. Shilov I., Seymour S., Patel A., Loboda A., Tang W., Keating S., et al. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 2007, 6:1638-1655.
32. Cui C., Churchchill G. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 2003, 4:210.
33. Mi H., Muruganujan A., Thomas P.D. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013, 41:D377-D386.
34. Frewen B.E., Merrihew G.E., Wu C.C., Noble W.S., MacCoss M.J. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem 2006, 78:5678-5684.
35. Frewen B., MacCoss M. Using BiblioSpec for creating and searching tandem MS peptide libraries. Curr Protoc Bioinformatics 2007, 13. Unit 13.7.
36. Gillet L., Navarro P., Tate S., Röst H., Selevsek N., Reiter L., et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012, 11. O111.016717.
37. Kanehisa M., Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30.
38. Joshi-Tope G., Gillespie M., Vastrik I., D'Eustachio P., Schmidt E., de Bono B., et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33:D428-D432.
39. Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011, 39:D561-D568.
40. Orchard S., Binz P., Borchers C., Gilson M., Jones A., Nicola G., et al. Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego USA. Proteomics 2012, 12:2767-2772.