MS-GF

* Introduction
MS-GF is a software to generate rigorous p-values (spectral probabilities) of spectral interpretations. Given peptide-spectrum matches (e.g. InsPecT result) as input, MS-GF outputs p-values that can be used to discriminate correct and false identifications. Currently, MS-GF supports InsPecT output and simplified version of InsPecT output (described below).
* Installation
Download MSGF.jar and place it in any folder. JRE 1.6 or greater must be installed to run MS-GF.
* Run
usage: java -Xmx2000M -jar MSGF.jar  -i ResultFile -d SpecDir [-o OutputFileName] (Default: stdout) [-m FragmentationMethod 0/1] (0: CID (default), 1: ETD) [-e Enzyme 0/1/2/3/4/5/6/7] (0: No enzyme, 1: Trypsin (default), 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N) [-fixMod 0/1/2] (0: NoCysteineProtection, 1: CarbamidomethyC (default), 2: CarboxymethylC) [-aaSet AASetFileName (default: standard amino acids)] [-x 0/1] (0: all (default), 1: OnePerSpec) [-p SpecProbThreshold] (Default: 1) [-param ScoringParamFile]
- "-Xmx2000M": specify maximum heap size allowed to JVM. For MS-GF, it is recommended to use more than 1000M. 
- ResultFile: tab-delimited file containing Peptide-Spectrum matches. InsPecT output file may be used as it is. To use it with other tools (e.g. Mascot or SEQUEST), one must make a "simplified InsPecT result file" using the following rules:
1) The file must be tab-delimited.
2) The first line must be the header starting with "#" and include #SpectrumFile, Scan#, Annotation and Charge. It may have other (optional) fields.
3) Each line (other than the first line) represents a peptide-spectrum match.
4) #SpectrumFile represents the spectrum file name. Only the file name (not the full path) will be recognized and later be searched in the directory specified with "-d" option. Currently mzXML (.mzXML), mgf (.mgf), ms2 (.ms2) and pkl (.pkl) formats are supported.
5) Scan# represents the spectrum position in the file. In the mzXML format, it must be the scan number. For all other formats, it is the zero-based sequential number of the spectrum in the file (e.g. the second spectrum in a mgf file will have value 1).
6) Annotation represents the peptide identification. It must have flanking amino acids delimited by '.'. To represent the start/end position of a protein, '*' (or any non-alphabetic character) must be used (e.g. *.ACDEFGHIR.A).
7) Charge represents the precursor charge of the spectrum. It must be positive integer.
=========
Example input file
#SpectrumFile   Title   Scan#   Annotation      Charge  Protein
/data/spec1.mgf Frac1 456 R.PEPTIDEK.G 2 Prot1
# Lines starting with # will be ignored.
spec2.mzXML Frac2 512 *.ACDEFGHIR.A 3 Prot2
...
=========
- SpecDir: the directory path (absolute or relative) that contains all the spectrum files.
- OutputFileName: output file name. MS-GF will add "SpecProb" column. If not specified, output will be sent to stdout. SpecProb times the number of residues in the database (you have used to get the PSM) approximates the E-value.
=========
Example output:
#SpectrumFile   Title   Scan#   Annotation      Charge  Protein SpecProb
/data/spec1.mgf Frac1 456 R.PEPTIDEK.G 2 Prot1 1.23E-4
spec2.mzXML Frac2 512 *.ACDEFGHIR.A 3 Prot2 4.12E-12
=========
- FragmentationMethod: fragmentation method. Scoring parameters will be chosen depending on this.
- Enzyme: enzyme used.
- "-fixMod": fixed modification.
- AASetFileName: a file containing amino acid information (e.g. see "AASetC57.txt"). 
- "-x": if "-x 1" is specified, only the best interpretation per spectrum will be printed.
- "-p SpecProbThreshold": if specified, only PSMs with equal or less than "SpecProbThreshold" will be printed.
- ScoringParamFile: path to the custom scoring parameter file. See below on how to make scoring parameter files.
* Generating a scoring parameter file
usage: 
java -Xmx2000M -cp MSGF.jar -i AnnotatedMgf (*.mgf) -o OutputParamFile (e.g. CID_Tryp.param) [-fixMod 0/1/2] (0: NoCysProtection, 1:CarbamidomethylC (default), 2: CarboxymethylC)
- AnnotatedMgf: mgf file containing annotations as "SEQ=" fields.
==========
Example:
BEGIN IONS
TITLE=022008_F11_ETD_1.mzXML:5111 interprophet=1.0
SEQ=GHGFEGVTHRWGTK
PEPMASS=523.59644
SCANS=5111
CHARGE=+3
143.3189        5.750927
158.71844       1.6126348
169.16019       2.5660455
....
END IONS
==========
- OutputParamFile: output parameter file name. The resulting parameter file can be used with "-param" option when running MS-GF.
- "-fixMod": fixed modification.
* Introduction

MS-GF is a software to generate rigorous p-values (spectral probabilities) of spectral interpretations. Given peptide-spectrum matches (e.g. InsPecT result) as input, MS-GF outputs p-values that can be used to discriminate correct and false identifications. Currently, MS-GF supports InsPecT output and simplified version of InsPecT output (described below).

* Installation

Download MSGF.jar and place it in any folder. JRE 1.6 or greater must be installed to run MS-GF.

* Run

usage: java -Xmx2000M -jar MSGF.jar 

-i ResultFile

-d SpecDir

[-o OutputFileName] (Default: stdout)

[-m FragmentationMethod 0/1] (0: CID (default), 1: ETD)

[-e Enzyme 0/1/2/3/4/5/6/7] (0: No enzyme, 1: Trypsin (default), 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N)

[-fixMod 0/1/2] (0: NoCysteineProtection, 1: CarbamidomethyC (default), 2: CarboxymethylC)

[-aaSet AASetFileName (default: standard amino acids)]

[-x 0/1] (0: all (default), 1: OnePerSpec)

[-p SpecProbThreshold] (Default: 1)

[-param ScoringParamFile]

- "-Xmx2000M": specify maximum heap size allowed to JVM. For MS-GF, it is recommended to use more than 1000M. 

- ResultFile: tab-delimited file containing Peptide-Spectrum matches. InsPecT output file may be used as it is. To use it with other tools (e.g. Mascot or SEQUEST), one must make a "simplified InsPecT result file" using the following rules:

1) The file must be tab-delimited.

2) The first line must be the header starting with "#" and include #SpectrumFile, Scan#, Annotation and Charge. It may have other (optional) fields.

3) Each line (other than the first line) represents a peptide-spectrum match.

4) #SpectrumFile represents the spectrum file name. Only the file name (not the full path) will be recognized and later be searched in the directory specified with "-d" option. Currently mzXML (.mzXML), mgf (.mgf), ms2 (.ms2) and pkl (.pkl) formats are supported.

5) Scan# represents the spectrum position in the file. In the mzXML format, it must be the scan number. For all other formats, it is the zero-based sequential number of the spectrum in the file (e.g. the second spectrum in a mgf file will have value 1).

6) Annotation represents the peptide identification. It must have flanking amino acids delimited by '.'. To represent the start/end position of a protein, '*' (or any non-alphabetic character) must be used (e.g. *.ACDEFGHIR.A).

7) Charge represents the precursor charge of the spectrum. It must be positive integer.

=========

Example input file

#SpectrumFile   Title   Scan#   Annotation      Charge  Protein

/data/spec1.mgfFrac1456R.PEPTIDEK.G2Prot1

# Lines starting with # will be ignored.

spec2.mzXMLFrac2512*.ACDEFGHIR.A3Prot2

...

=========

- SpecDir: the directory path (absolute or relative) that contains all the spectrum files.

- OutputFileName: output file name. MS-GF will add "SpecProb" column. If not specified, output will be sent to stdout. SpecProb times the number of residues in the database (you have used to get the PSM) approximates the E-value.

=========

Example output:

#SpectrumFile   Title   Scan#   Annotation      Charge  ProteinSpecProb

/data/spec1.mgfFrac1456R.PEPTIDEK.G2Prot11.23E-4

spec2.mzXMLFrac2512*.ACDEFGHIR.A3Prot24.12E-12

=========

- FragmentationMethod: fragmentation method. Scoring parameters will be chosen depending on this.

- Enzyme: enzyme used.

- "-fixMod": fixed modification.

- AASetFileName: a file containing amino acid information (e.g. see "AASetC57.txt"). 

- "-x": if "-x 1" is specified, only the best interpretation per spectrum will be printed.

- "-p SpecProbThreshold": if specified, only PSMs with equal or less than "SpecProbThreshold" will be printed.

- ScoringParamFile: path to the custom scoring parameter file. See below on how to make scoring parameter files.

* Generating a scoring parameter file

usage: 

java -Xmx2000M -cp MSGF.jar

-i AnnotatedMgf (*.mgf)

-o OutputParamFile (e.g. CID_Tryp.param)

[-fixMod 0/1/2] (0: NoCysProtection, 1:CarbamidomethylC (default), 2: CarboxymethylC)

- AnnotatedMgf: mgf file containing annotations as "SEQ=" fields.

==========

Example:

BEGIN IONS

TITLE=022008_F11_ETD_1.mzXML:5111 interprophet=1.0

SEQ=GHGFEGVTHRWGTK

PEPMASS=523.59644

SCANS=5111

CHARGE=+3

143.3189        5.750927

158.71844       1.6126348

169.16019       2.5660455

....

END IONS

==========

- OutputParamFile: output parameter file name. The resulting parameter file can be used with "-param" option when running MS-GF.

- "-fixMod": fixed modification.

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