MSFileParser

Perl library to parse Mass Spectrometry text based file formats

Supported Formats

File Format	File extension	Standard Type	File Type	Format Type	Module
MGF (Mascot genetic format)	.mgf	De facto	Text	Input MS/MS spectra	MSFileParser.pm
mzML	.mzML	HUPO-PSI	XML	Input MS/MS spectra (HUPO standard)	mzMLParser.pm
Tandem XML	.t.xml	De facto X!Tandem output	XML	Search result	PSMFileIO.pm
pepXML	.pep.xml	De facto TPP output	XML	Search result	PepXMLParser.pm
mzIdentML	.mzid	HUPO-PSI	XML	Search result (HUPO standard)	mzIdentMLParser.pm
Pkl (Waters MassLynx peak list format)	.pkl	De facto	Text	Input MS/MS spectra	MSFileParser
DTA	.dta	De facto	Text	Input MS/MS spectra	MSFileParser
mzQuantML	.mzq	HUPO-PSI	XML	Quantitation result	mzMLQuant.pm
mzTab	.mztab	HUPO-PSI	Text/Tab	Identification/QUantification	mzTab.pm
mzQc	.mzqc	HUPO-PSI	XML	QC data	mzQc.pm
mzPAF	.mzqc	HUPO-PSI	XML	Peak Annotation Format	mzPAF.pm
mzSpecLib	.mzsplib	HUPO-PSI	Text	Spectral library text format	mzSpecLib.pm
miXML	.miXML	HUPO-PSI	XML	Molecular Interactions Exchange Format	miXML.pm
miTab	.miTab	HUPO-PSI	Text	Molecular Interactions in Tab Format	miTab.pm

Example Use cases

Please note that the library will provide data strcutures for further processing. The choice of algorithms (third-party or user-developed) is out of the current scope, even though some examples are provided.

Before search (uninterpreted spectra)

• Deisotoping
• Peak picking from raw MS/MS spectra
• Noise removal
• Spectra filtering and selection based on diagnostic ions
• de novo sequencing
• PTM-specific spectra filtering

Spectra search (MS/MS based matching)

• MS/MS peptide matching
• PTM site localization
• PTM identification
• iTRAQ quantitation
• TMT quantitation

Post-search analysis

• FDR estimation
• integrating search results from multiple algorithms
• visualization

Help and Support

For help with the library or use cases, please use the issues tracker.

Email

For further support, please email amit.yadav@thsti.res.in