Visualization of LC-MS/MS proteomics data in MaxQuant

Proteomics

Volumn 15, Issue 8, 2015, Pages 1453-1456

  Tyanova, Stefka ^a   Temu, Tikira ^a   Carlson, Arthur ^a   Sinitcyn, Pavel ^a   Mann, Matthias ^a   Cox, Juergen ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Bioinformatics; LC MS MS; Mass spectrometry; Visualization

Indexed keywords

ARTICLE; AUTOMATION; COMPUTER PROGRAM; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MAXQUANT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; THREE DIMENSIONAL IMAGING; AMINO ACID SEQUENCE; COMPUTER GRAPHICS; PROCEDURES; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; CHROMATOGRAPHY, LIQUID; COMPUTER GRAPHICS; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84926514125     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400449     Document Type: Article

References (11)

1. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
2. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
3. Michalski, A., Cox, J., Mann, M., More than 100000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 2011, 10, 1785-1793.
4. Geiger, T., Cox, J., Mann, M., Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell. Proteomics 2010, 9, 2252-2261.
5. 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.
6. Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., Heck, A. J., Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protocols 2009, 4, 484-494.
7. Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B. et al., PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40, D261-D270.
8. 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.
9. UniProt Consortium, Activities at the universal protein resource (UniProt). Nucleic Acids Res. 2014, 42, D191-D198.
10. Finn, R. D., Bateman, A., Clements, J., Coggill, P. et al., Pfam: the protein families database. Nucleic Acids Res. 2014, 42, D222-D230.
11. Cox, J., Hein, M. Y., Luber, C. A., Paron, I. et al., Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 2014, 13, 2513-2526.