An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQTM

Proteome Science

Volumn 5, Issue , 2007, Pages

  Siepen, Jennifer A ^a   Swainston, Neil ^a   Jones, Andrew R ^a   Hart, Sarah R ^a   Hermjakob, Henning ^b   Jones, Philip ^b   Hubbard, Simon J ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

ARTICLE; BIOINFORMATICS; COMPUTER LANGUAGE; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; INTERNET; PEPTIDE ANALYSIS; PRODUCT DEVELOPMENT; PROTEIN DATABASE; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SAMPLE SIZE; TECHNOLOGY;

EID: 33847240073     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-5-4     Document Type: Article

References (32)

1. 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 Molecular & Cellular Proteomics 2002 1 5 376-386 10.1074/mcp.M200025-MCP200
2. Gerber SA Rush J Stemman O Kirschner MW Gygi SP Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proceedings of the National Academy of Sciences of the United States of America 2003 100 12 6940-6945 165809 12771378 10.1073/pnas.0832254100
3. Gygi SP Rist B Gerber SA Turecek F Gelb MH Aebersold R Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nature Biotechnology 1999 17 10 994-999 10.1038/13690 10504701
4. Ross PL Huang YLN 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 Molecular & Cellular Proteomics 2004 3 12 1154 1169 10.1074/ mcp.M400129-MCP200
5. Beynon RJ Doherty MK Pratt JM Gaskell SJ Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides Nature Methods 2005 2 8 587-589 10.1038/ nmeth774 16094383
6. Pratt JM Simpson D Doherty M Rivers J Gaskell SJ Beynon RJ Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes Nature Protocols 2006 1 1029-1043 10.1038/nprot.2006.129
7. de Godoy LMF Olsen JV de Souza GA Li GQ Mortensen P Mann M Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system Genome Biology 2006 7 6 1779535 16784548
8. Pedrioli PGA 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 Kapp E McComb ME Oliver SG Omenn G Paton NW Simpson R Smith R Taylor CF Zhu WM Aebersold R A common open representation of mass spectrometry data and its application to proteomics research Nature Biotechnology 2004 22 11 1459 1466 10.1038/nbt1031 15529173
9. Taylor CF Hermjakob H Julian RK Garavelli JS Aebersold R Apweiler R The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI) Omics - a Journal of Integrative Biology 2006 10 2 145-151 10.1089/omi.2006.10.145 16901219
10. Hermjakob H Montecchi-Palazzi L Bader G Wojcik R Salwinski L Ceol A Moore S Orchard S Sarkans U von Mering C Roechert B Poux S Jung E Mersch H Kersey P Lappe M Li YX Zeng R Rana D Nikolski M Husi H Brun C Shanker K Grant SGN Sander C Bork P Zhu WM Pandey A Brazma A Jacq B Vidal M Sherman D Legrain P Cesareni G Xenarios L Eisenberg D Steipe B Hogue C Apweiler R The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data Nature Biotechnology 2004 22 2 177-183 10.1038/nbt926 14755292
11. Jones AR Miller M Aebersold R Apweiler R Ball CA Brazma A DeGreef J Hardy N Hermjakob H Hubbard SJ Hussey P Igra M Jenkins H Julian RK Laursen K Oliver SG Paton NW Sarkans U Sansone S Stoeckert CJ Taylor CF Whetzel PL White JA Spellman P Piazarro A The functional genomics experimental model (FuGE): An extensible framework for standards in functional genomics. Nature Biotechnology 2006 in press.
12. Jones AR Paton NW An analysis of extensible modelling for functional genomics data Bmc Bioinformatics 2005 6
13. Prince JT Carlson MW Wang R Lu P Marcotte EM The need for a public proteomics repository Nature Biotechnology 2004 22 4 471-472 10.1038/ nbt0404-471 15085804
14. 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 2006 34 D655-D658 1347403 16381952 10.1093/nar/gkj040
15. Craig R Cortens JP Beavis RC Open source system for analyzing, validating, and storing protein identification data Journal of Proteome Research 2004 3 6 1234-1242 10.1021/pr049882h 15595733
16. McLaughlin T Siepen JA Selley J Lynch JA Lau KW Yin HJ Gaskell SJ Hubbard SJ PepSeeker: A database of proteome peptide identifications for investigating fragmentation patterns Nucleic Acids Research 2006 34 D649-D654 1347429 16381951 10.1093/nar/gkj066
17. Garwood K McLaughlin T Garwood C Joens S Morrison N Taylor CF Carroll K Evans C Whetton AD Hart S Stead D Yin Z Brown AJP Hesketh A Chater K Hansson L Mewissen M Ghazal P Howard J Lilley KS Gaskell SJ Brass A Hubbard SJ Oliver SG Paton NW PEDRo: A database for storing, searching and disseminating experimental proteomics data Bmc Genomics 2004 5 521486 15377392
18. Martens L Hermjakob H Jones P Adamski M Taylor C States D Gevaert K Vandekerckhove J Apweiler R PRIDE: The proteomics identifications database Proteomics 2005 5 13 3537-3545 10.1002/pmic.200401303 16041671
19. Orchard S Hermjakob H Taylor CF Potthost F Jones P Zhu WM Julian RK Apweiler R Second Proteomics Standards Initiative Spring Workshop Expert Review of Proteomics 2005 2 3 287-289 10.1586/14789450.2.3.287 16000075
20. Jones P Cote RG Martens L Quinn AF Taylor CF Derache W Hermjakob H Apweiler R PRIDE: A public repository of protein and peptide identifications for the proteomics community Nucleic Acids Research 2006 34 D659-D663 1347500 16381953 10.1093/nar/gkj138
21. Cote RG Jones P Apweiler R Hermjakob H The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries Bmc Bioinformatics 2006 7 1420335 16507094
22. Falkner JA Ulintz PJ Andrews PC http://www.proteomecommons.org/
23. Shadforth IP Dunkley TPJ Lilley KS Bessant C i-Tracker: For quantitative proteomics using iTRAQ (TM) Bmc Genomics 2005 6 145 1276793 16242023 10.1186/1471-2164-6-145
24. Creasy DM Cottrell JS Unimod: Protein modifications for mass spectrometry Proteomics 2004 4 6 1534-1536 10.1002/pmic.200300744 15174123
25. PrideWizard http://www.mcisb.org/software/PrideWizard
26. PedroDC Capture Tool http://pedrodownload.man.ac.uk
27. Perkins DN Pappin DJC Creasy DM Cottrell JS Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999 20 18 3551-3567 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
28. Phan IQH Pilbout SF Fleischmann W Bairoch A NEWT, a new taxonomy portal Nucleic Acids Research 2003 31 13 3822-3823 168923 12824428 10.1093/nar/ gkg516
29. Broadhead R Dawe HR Farr H Griffiths S Hart SR Portman N Shaw MK Ginger ML Gaskell SJ McKean PG Gull K Flagellar motility is required for the viability of the bloodstream trypanosome Nature 2006 440 7081 224-227 10.1038/nature04541 16525475
30. Coulthurst SJ Lilley KS Salmond GPC Genetic and proteomic analysis of the role of luxS in the enteric phytopathogen, Erwinia carotovora Molecular Plant Pathology 2006 7 1 31-45 10.1111/j.1364-3703.2005.00314.x
31. Dunkley TPJ Hester S Shadforth IP Runions J Weimar T Hanton SL Griffin JL Bessant C Brandizzi F Hawes C Watson RB Dupree P Lilley KS Mapping the Arabidopsis organelle proteome Proceedings of the National Academy of Sciences of the United States of America 2006 103 17 6518-6523 1458916 16618929 10.1073/pnas.0506958103
32. Unwin RD Smith DL Blinco D Wilson CL Miller CJ Evans CA Jaworska E Baldwin SA Barnes K Pierce A Spooncer E Whetton AD Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells Blood 2006 107 12 4687-4694 10.1182/ blood-2005-12-4995 16507774