MS2 file format
The MS2 file format is used to record MS/MS spectra. A full description of the MS2 file format may be found in: McDonald,W.H. et al. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18, 2162-2168 (2004).
An MS2 file consists of a header followed by one or more sets of scan data. The header and scan data are broken into records, one record per line. The fields within a record are separated by white space. The header records list information applicable to all the scans in the file. Each scan begins with a few records describing the parameters for that scan. This is followed by pairs of m/z and intensity values, one pair per line.
A sample MS2 file may be found here.
Each line in the header must begin with an
H. This is followed by a field label, and then a field value, all separated by white space. The field label must be one of the labels listed below, while the field value can be an aribrary string. A typical header is shown below.H CreationDate 2/14/2007 6:19:18 PM H Extractor MakeMS2 H ExtractorVersion 1.0 H Comments MakeMS2 written by Michael J. MacCoss, 2004 H ExtractorOptions MS2/MS1
The following field labels must appear in the header:
Required header field labels Field Label Description CreationDate The date and time when the file was created Extractor The name of the software used to create the MS2 file ExtractorVersion The version number of the Extractor software ExtractorOptions The options used in running the extractor software
The following field labels are optional, and may appear in the header:
Optional header field labels Field Label Description IAnalyzer Name of software used to conduct charge-state independent analysis of the spectra IAnalyzerVersion The version number of the IAnalyzer software IAnalyzerOptions The options used in running the IAnalyzer software DAnalyzer Name of software used to conduct charge-state dependent analysis of the spectra DAnalyzerVersion The version number of the DAnalyzer software DAnalyzerOptions The options used in running the DAnalyzer software SortedBy Name of field use to sort spectra InstrumentType The type of mass analyzer used Comment Remarks. Multiple comment lines are allowed InstrumentSN Serial number of the mass spectrometer used
Each scan begins with a few records listing the parameters describing the spectrum. These lines must begin with S, I, Z, or D. The records are followed by pairs of m/z and intensity values, one pair per line. A fragment of a typical scan is shown below.S 10 10 636.34 Z 2 1271.67 187.4 12.5 193.1 19.5 194.3 13.7 198.3 29.8 199.1 12.2
Record types for scans Symbol Description Generic form Required S scan
S [first scan] [second scan] [pre m/z]
yes I Charge independent analysis
I [field label] [field value]
no Z Charge
I [charge] [mass]
yes D Charge dependent analysis
I [field label] [field value]
no [data] m/z intensity paris [m/z] [intensity] yes
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