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.

Header details

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

Scan details

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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