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:
| 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:
| 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
| 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 |