PhosFox: A bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

Proteome Science

Volumn 12, Issue 1, 2014, Pages

  Söderholm, Sandra ^a   Hintsanen, Petteri ^b   Öhman, Tiina ^a   Aittokallio, Tero ^b   Nyman, Tuula A ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Data processing and analysis; Database searching; LC MS MS; Phosphoproteomics

Indexed keywords

PHOSPHOPEPTIDE;

ACETYLATION; ARTICLE; BIOINFORMATICS; CELL DEATH; CELL SURVIVAL; HUMAN; HUMAN CELL; KERATINOCYTE; KIDNEY MEDULLA; LIQUID CHROMATOGRAPHY; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY;

RATTUS;

EID: 84902934717     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-12-36     Document Type: Article

References (33)

1. Lemeer S, Heck AJ. The phosphoproteomics data explosion. Curr Opin Chem Biol 2009, 13(4):414-420.
2. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20(18):3551-3567.
3. Eng JK, McCormack AL, Yates JRI. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5:976-989.
4. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9):1466-1467.
5. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH. Open mass spectrometry search algorithm. J Proteome Res 2004, 3(5):958-964.
6. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 2011, 10(4):1794-1805.
7. Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA. 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(9):1638-1655.
8. Jiang X, Ye M, Cheng K, Zou H. ArMone: a software suite specially designed for processing and analysis of phosphoproteome data. J Proteome Res 2010, 9(5):2743-2751.
9. Courcelles M, Lemieux S, Voisin L, Meloche S, Thibault P. ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses. Proteomics 2011, 11(13):2654-2671.
10. Bennetzen MV, Cox J, Mann M, Andersen JS. PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN. J Proteome Res 2012, 11(6):3480-3486.
11. Yu K, Salomon AR. PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. Proteomics 2009, 9(23):5350-5358.
12. Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B. Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 2011, 10(2):M110.003830.
13. Taus T, Kocher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K. Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 2011, 10(12):5354-5362.
14. Lietzen N, Natri L, Nevalainen OS, Salmi J, Nyman TA. Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon. J Proteome Res 2010, 9(12):6795-6800.
15. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3(12):1154-1169.
16. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1(5):376-386.
17. Ohman T, Lietzen N, Valimaki E, Melchjorsen J, Matikainen S, Nyman TA. Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes. J Proteome Res 2010, 9(3):1549-1564.
18. Villen J, Gygi SP. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 2008, 3(10):1630-1638.
19. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127(3):635-648.
20. Luo R, Fang L, Jin H, Wang D, An K, Xu N, Chen H, Xiao S. Label-free quantitative phosphoproteomic analysis reveals differentially regulated proteins and pathway in PRRSV-infected pulmonary alveolar macrophages. J Proteome Res 2014, 13(3):1270-1280.
21. Hoffert JD, Pisitkun T, Saeed F, Song JH, Chou CL, Knepper MA. Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics. Mol Cell Proteomics 2012, 11(2):M111.014613.
22. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504.
23. Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics 2009, 25(5):684-686.
24. Kawakami T, Kawakami Y, Kitaura J. Protein kinase C beta (PKC beta): normal functions and diseases. J Biochem 2002, 132(5):677-682.
25. Timm T, Marx A, Panneerselvam S, Mandelkow E, Mandelkow EM. Structure and regulation of MARK, a kinase involved in abnormal phosphorylation of Tau protein. BMC Neurosci 2008, 9(Suppl 2):S9. http://www.ncbi.nlm.nih.gov/pubmed/19090997.
26. Davis AJ, Lee KJ, Chen DJ. The N-terminal region of the DNA-dependent protein kinase catalytic subunit is required for its DNA double-stranded break-mediated activation. J Biol Chem 2013, 288(10):7037-7046.
27. Melchjorsen J, Sorensen LN, Paludan SR. Expression and function of chemokines during viral infections: from molecular mechanisms to in vivo function. J Leukoc Biol 2003, 74(3):331-343.
28. Mikkelsen SS, Jensen SB, Chiliveru S, Melchjorsen J, Julkunen I, Gaestel M, Arthur JS, Flavell RA, Ghosh S, Paludan SR. RIG-I-mediated activation of p38 MAPK is essential for viral induction of interferon and activation of dendritic cells: dependence on TRAF2 and TAK1. J Biol Chem 2009, 284(16):10774-10782.
29. Stahl JA, Chavan SS, Sifford JM, Macleod V, Voth DE, Edmondson RD, Forrest JC. Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication. PLoS Pathog 2013, 9(9):e1003583.
30. Wojcechowskyj JA, Didigu CA, Lee JY, Parrish NF, Sinha R, Hahn BH, Bushman FD, Jensen ST, Seeholzer SH, Doms RW. Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry. Cell Host Microbe 2013, 13(5):613-623.
31. Popova TG, Turell MJ, Espina V, Kehn-Hall K, Kidd J, Narayanan A, Liotta L, Petricoin EF3, Kashanchi F, Bailey C, Popov SG. Reverse-phase phosphoproteome analysis of signaling pathways induced by Rift valley fever virus in human small airway epithelial cells. PLoS One 2010, 5(11):e13805.
32. Lietzen N, Ohman T, Rintahaka J, Julkunen I, Aittokallio T, Matikainen S, Nyman TA. Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages. PLoS Pathog 2011, 7(5):e1001340.
33. Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2013, 41(Database issue):D1063-D1069.