Introduction

Extraction of data from the proprietary RAW files generated by Thermo Fisher mass spectrometers is the primary step for subsequent data analysis. High resolution and high mass accuracy data obtained by state-of-the-art mass spectrometers (e.g., Orbitraps) can significantly improve both peptide/protein identification and quantification. We developed RawConverter, a stand-alone software tool, to improve data extraction on RAW files from high-resolution Thermo Fisher mass spectrometers. RawConverter extracts full scan and MS(n) data from RAW files like its predecessor RawXtract; most importantly, it associates the accurate precursor mass-to-charge (m/z) value with the tandem mass spectrum. RawConverter accepts RAW data generated by either data-dependent acquisition (DDA) or data-independent acquisition (DIA). It generates output into MS1/MS2/MS3, MGF, or mzXML file formats, which fulfills the format requirements for most data identification and quantification tools. Using the tandem mass spectra extracted by RawConverter with corrected m/z values, 32.8%, 27.1%, and 84.1%, peptide spectra matches (PSMs) produce 17.4% (13.0%), 14.4% (11.5%), and 45.7% (36.2%) more peptide (protein) identifications than ProteoWizard, pXtract, and RawXtract, respectively. RawConverter is implemented in C# and is freely accessible at http://fields.scripps.edu/rawconv.

Publications

  1. Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter.
    Cite this
    He L, Diedrich J, Chu YY, Yates JR 3rd, 2015-11-01 - Analytical chemistry
  2. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.
    Cite this
    McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR 3rd, 2004-01-01 - Rapid communications in mass spectrometry : RCM

Credits

  1. Lin He
    Developer

    Department of Chemical Physiology, The Scripps Research Institute, United States of America

  2. Jolene Diedrich
    Developer

    Department of Chemical Physiology, The Scripps Research Institute, United States of America

  3. Yen-Yin Chu
    Developer

    Department of Communication Engineering, National Central University, Taiwan, Province of China

  4. John R Yates
    Investigator

    Department of Chemical Physiology, The Scripps Research Institute, United States of America

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Summary
AccessionBT000390
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJohn R Yates