Employing ProteoWizard to convert raw mass spectrometry data

Current Protocols in Bioinformatics

Volumn , Issue SUPPL.46, 2014, Pages

  Holman, Jerry D ^a   Tabb, David L ^a   Mallick, Parag ^b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Database search; LC MS MS; mzML; Proteomics; Raw files

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRACTICE GUIDELINE; PRIORITY JOURNAL; SEARCH ENGINE; PROTEIN DATABASE; SOFTWARE; TANDEM MASS SPECTROMETRY;

DATABASES, PROTEIN; SOFTWARE; TANDEM MASS SPECTROMETRY; USER-COMPUTER INTERFACE;

EID: 84940241156     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi1324s46     Document Type: Article

References (7)

1. Chambers, M.C., Maclean, B., Burke, R., Amodei, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L., and Mallick, P. 2012. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30:918-920.
2. Eng, J.K., McCormack, A.L., and Yates, J.R. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976-989.
3. Eng, J.K., Jahan, T.A., and Hoopmann, M.R. 2013. Comet: An open-source MS/MS sequence database search tool. Proteomics 13:22-24.
4. Kessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. 2008. ProteoWizard: Open source software for rapid proteomics tools development. Bioinformatics 24:2534-2536.
5. Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W. H., R̈ompp, A., Neumann, S., Pizarro, A. D., Montecchi-Palazzi, L., Tasman, N., Coleman, M., Reisinger, F., Souda, P., Hermjakob, H., Binz, P.A., and Deutsch, E.W. 2011. mzML- A community standard for mass spectrometry data. Mol. Cell. Proteomics 10:R110.000133.
6. Pedrioli, P.G.A., Eng, J.K., Hubley, R., Vogelzang, M., Deutsch, E.W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R.H., Apweiler, R., Cheung, K., Costello, C.E., Hermjakob, H., Huang, S., Julian, R.K., Kapp, E., McComb, M.E., Oliver, S.G., Omenn, G., Paton, N.W., Simpson, R., Smith, R., Taylor, C.F., Zhu, W., and Aebersold, R. 2004. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22:1459-1466.
7. Wilhelm, M.,Kirchner, M., Steen, J.A.J., and Steen, H. 2012. mz5: Space- and time-efficient storage of mass spectrometry data sets. Mol. Cell. Proteomics 11:O111.011379.