Extracting accurate precursor information for tandem mass spectra by RawConverter

L He, J Diedrich, YY Chu, JR Yates III - Analytical chemistry, 2015 - ACS Publications
L He, J Diedrich, YY Chu, JR Yates III
Analytical chemistry, 2015ACS Publications
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 (eg, 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 …
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 MSn 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.
ACS Publications