He Lin, Diedrich Jolene, Chu Yen-Yin, Yates John R
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.
Anal Chem. 2015 Nov 17;87(22):11361-7. doi: 10.1021/acs.analchem.5b02721. Epub 2015 Nov 4.
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.
从赛默飞世尔质谱仪生成的专有RAW文件中提取数据是后续数据分析的首要步骤。通过最先进的质谱仪（如轨道阱）获得的高分辨率和高质量精度数据可以显著提高肽段/蛋白质的鉴定和定量。我们开发了RawConverter，这是一个独立的软件工具，用于改进从高分辨率赛默飞世尔质谱仪的RAW文件中提取数据。RawConverter像其前身RawXtract一样从RAW文件中提取全扫描和MS(n)数据；最重要的是，它将准确的前体质荷比（m/z）值与串联质谱相关联。RawConverter接受通过数据依赖采集（DDA）或数据独立采集（DIA）生成的RAW数据。它生成MS1/MS2/MS3、MGF或mzXML文件格式的输出，满足大多数数据鉴定和定量工具的格式要求。使用RawConverter提取的具有校正m/z值的串联质谱，肽谱匹配（PSM）分别比ProteoWizard、pXtract和RawXtract多产生17.4%（13.0%）、14.4%（11.5%）和45.7%（36.2%）的肽段（蛋白质）鉴定结果。RawConverter用C#实现，可在http://fields.scripps.edu/rawconv免费获取。
