Laboratory Data and Sample Management for Proteomics

Methods in Molecular Biology

Volumn 696, Issue , 2011, Pages 79-92

  Häkkinen, Jari ^a   Levander, Fredrik ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Annotation Type; Decoy Database; Laboratory Information Management System; Search Engine; Search Result

Indexed keywords

PROTEOMICS; SEARCH ENGINE; SOFTWARE; WORKFLOW; ARTICLE; COMPUTER PROGRAM; DATA BASE; HOSPITAL INFORMATION SYSTEM; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METHODOLOGY; PROTEIN DATABASE; TWO DIMENSIONAL GEL ELECTROPHORESIS;

CHROMATOGRAPHY, LIQUID; CLINICAL LABORATORY INFORMATION SYSTEMS; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; MASS SPECTROMETRY; PROTEOMICS; SOFTWARE;

MLCS; MLOWN;

EID: 79952201416     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-987-1_5     Document Type: Chapter

References (14)

1. Hamacher M, Stephan C, Meyer HE, Eisenacher M (2009) Data handling and processing in proteomics. Expert Rev Proteomics 6:217–219
2. Piggee C (2008) LIMS and the art of MS proteomics. Anal Chem 80:4801–4806
3. Häkkinen J, Vincic G, Månsson O, Wårell K, Levander F (2009) The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. J Proteome Res 8:3037–3043
4. Stephan, C., Kohl, M., Turewicz, M., Podwojski, K., Meyer, H.E., Eisenacher, M (2010) Using laboratory information management systems as central part of a proteomics data workflow. Proteomics 10:1230–1249
5. Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D et al (2005) PRIDE: The proteomics identifications database. Proteomics 5:3537–3545
6. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G et al (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75:1895–1904
7. Orchard S, Taylor C, Hermjakob H, Zhu W, Julian R, Apweiler R (2004) Current status of proteomic standards development. Expert Rev Proteomics 1:179–183
8. Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., et al. (2010) mzML – A community standard for mass spectrometry Mol Cell Proteomics doi:10.1074/mcp.R110.000133
9. Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008) Proteowizard: open source software for rapid proteomics tools development. Bioinformatics 24:2534–2536
10. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Meth 4:207–214
11. Levander F, Krogh M, Wårell K, Gärdén P, James P, Häkkinen J (2007) Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 7:668–674
12. Reidegeld KA, Eisenacher M, Kohl M, Chamrad D, Korting G, Blueggel M et al (2008) An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications. Proteomics 8:1129–1137
13. Wilkins MR, Appel RD, Van Eyk JE, Chung MCM, Gorg A, Hecker M et al (2006) Guidelines for the next 10 years of proteomics. Proteomics 6:4–8
14. Taylor CF, Paton NW, Lilley KS, Binz P-A, Julian RK, Jones AR et al (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25:887–893