Employing ProteoWizard to Convert Raw Mass Spectrometry Data

Jerry D. Holman1, David L. Tabb1, Parag Mallick2

1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, 2 Department of Radiology, Stanford School of Medicine, Palo Alto, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.24
DOI:  10.1002/0471250953.bi1324s46
Online Posting Date:  June, 2014
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After raw data have been captured by mass spectrometers in biological LC‐MS/MS experiments, they must be converted from vendor‐specific binary files to open‐format files for manipulation by most software. This protocol details the use of ProteoWizard software for this conversion, taking format features, coding options, and vendor particularities into account. This protocol will aid researchers in preparing their data for analysis by database search engines and other bioinformatics tools. Curr. Protoc. Bioinform. 46:13.24.1‐13.24.9. © 2014 by John Wiley & Sons, Inc.

Keywords: LC‐MS/MS; mzML; database search; raw files; proteomics

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Table of Contents

  • Introduction
  • Basic Protocol 1: Transcoding MS Data from Raw Format via MSConvert GUI
  • Alternate Protocol 1: Transcoding MS Data from Raw Format via MSConvert
  • Basic Protocol 2: Converting mzML Data to Simple Text Formats for Search Engines
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
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Literature Cited

Literature Cited
  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.
  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.
  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.
  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.
  Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W. H., Römpp, 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.
  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.
  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.
Key Reference
  Chambers et al., 2012. See above.
  Reporting updates during the first 5 years of the ProteoWizard project, this manuscript broadly summarizes the capabilities of these tools and libraries
Internet Resources
  ProteoWizard is available from this Web site.
  AB SCIEX provides the AB SCIEX MS Data Converter.
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