Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra

Journal of Proteomics

Volumn 95, Issue , 2013, Pages 89-92

  Hulstaert, Niels ^a,b   Reisinger, Florian ^c   Rameseder, Jonathan ^d,e   Barsnes, Harald ^f   Vizcaíno, Juan Antonio ^c   Martens, Lennart ^a,b  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d Massachusetts Institute of Technology Cambridge   (United States)

^e David H Koch Institute for Integrative Cancer Research   (United States)

^f UNIVERSITY OF BERGEN   (Norway)

Author keywords

Bioinformatics; Mass spectrometry; PRIDE; Proteomics

Indexed keywords

ION;

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS;

API; APPLICATION PROGRAMMING INTERFACE; ASAP; AUTOMATIC SPECTRUM ANNOTATION PIPELINE; BIOINFORMATICS; GRAPHICAL USER INTERFACE; GUI; MASS SPECTROMETRY; PEPTIDE SPECTRUM MATCH; POST-TRANSLATIONAL MODIFICATION; PRIDE; PROTEOMICS; PROTEOMICS IDENTIFICATIONS (DATABASE); PSM; PTM;

DATABASES, PROTEIN; INTERNET; IONS; PROTEOMICS; SOFTWARE;

EID: 84888301228     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.04.011     Document Type: Article

References (19)

1. Martens L., Hermjakob H., Jones P., Adamski M., Taylor C., States D., et al. PRIDE: the proteomics identifications database. Proteomics 2005, 5:3537-3545.
2. Jones P., Cote R.G., Martens L., Quinn A.F., Taylor C.F., Derache W., et al. PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 2006, 34:D659-D663.
3. Vizcaíno J.A., CÔté R., Reisinger F., Barsnes H., Foster J.M., Rameseder J., et al. The Proteomics Identifications database: 2010 update. Nucleic Acids Res 2010, 38:D736-D742.
4. Barsnes H., Vizcaíno J.A., Eidhammer I., Martens L. PRIDE converter: making proteomics data-sharing easy. Nat Biotechnol 2009, 27:598-599.
5. CÔté R.G., Griss J., Dianes J.A., Wang R., Wright J.C., van den Toorn H.W.P., et al. The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics 2013, (in press).
6. Helsens K., Martens L., Vandekerckhove J., Gevaert K. MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results. Proteomics 2007, 7:364-366.
7. Barsnes H., Huber S., Sickmann A., Eidhammer I., Martens L. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results. Proteomics 2009, 9:3772-3774.
8. Muth T., Vaudel M., Barsnes H., Martens L., Sickmann A. XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics 2010, 10:1522-1524.
9. Fan J., Mohareb F., Bond N.J., Lilley K.S., Bessant C. MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. OMICS 2012, 16:483-488.
10. Barsnes H., Eidhammer I., Martens L. FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics 2010, 10:1087-1090.
11. Wang R., Fabregat A., Ríos D., Ovelleiro D., Foster J.M., CÔté R.G., et al. PRIDE inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol 2012, 30:135-137.
12. Neuhauser N., Michalski A., Cox J., Mann M. Expert system for computer-assisted annotation of MS/MS spectra Mol. Cell Proteomics 2012, 11:1500-1509.
13. Hasings C., Mosteller F., Tukey J.W., Winsor C.P. Low moments for small samples: a comparative study of order statistics. Ann Math Stat 1947, 18:413-426.
14. R Core Team R: A Language and Environment for Statistical, Computing 2012.
15. Gonnelli G., Hulstaert N., Degroeve S., Martens L. Towards a human proteomics atlas. Anal Bioanal Chem 2012, 404:1069-1077.
16. Volders P., Helsens K., Wang X., Menten B., Martens L., Gevaert K., Vandesompele J., Mestdagh P. LNCipedia: a database for annotated human lncRNA transcript sequences and structures Nucleic Acids Res. 2013, 41:D246-D251.
17. Jones A.R., Eisenacher M., Mayer G., Kohlbacher O., Siepen J., Hubbard S.J., et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics 2012, 11. (M111.014381).
18. Foster J.M., Degroeve S., Gatto L., Visser M., Wang R., Griss J., et al. A posteriori quality control for the curation and reuse of public proteomics data. Proteomics 2011, 11:2182-2194.
19. Csordas A., Ovelleiro D., Wang R., Foster J.M., Ríos D., Vizcaíno J.A., et al. PRIDE: quality control in a proteomics data repository. Database (Oxford) 2012, 11:bas004.