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Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter

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Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
Department of Communication Engineering, National Central University, 300 Jung-da Road, Jung-li City, Taoyuan 32001, Taiwan
*Tel: +1 (858) 784-8862. Fax: +1 (858) 784-8883. E-mail: [email protected]
Cite this: Anal. Chem. 2015, 87, 22, 11361–11367
Publication Date (Web):October 26, 2015
https://doi.org/10.1021/acs.analchem.5b02721
Copyright © 2015 American Chemical Society

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    Abstract

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    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.

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