title: Employing ProteoWizard to Convert Raw Mass Spectrometry Data.
abstract: 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.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.
authors.forename: Jerry D
authors.initials: JD
authors.lastname: Holman
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.affiliation: Department of Radiology, Stanford School of Medicine, Palo Alto, California.
authors.forename: Parag
authors.initials: P
authors.lastname: Mallick
mesh_terms: D030562:Databases, Protein; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface
keywords: LC-MS/MS; database search; mzML; proteomics; raw files