MzidLib 1.3 / 1.4 Beta
MzIdentML library for manipulating data in the mzIdentML standard
MzidLib comes both as a command line tool and as a GUI tool. Also, all routines will export a new mzIdentML file.
· Omssa2Mzid (Omssa OMX to mzIdentML version 1.1 converter)
· Tandem2Mzid (X!Tandem XML to mzIdentML version 1.1 converter)
· Csv2Mzid (Converts Omssa CSV output to mzIdentML version 1.1) - this can be customized to convert other results in CSV format into mzIdentML
· emPAI - performs the emPAI quantitation protocol and inserts results into a new mzIdentML file
· FalseDiscoveryRate - calculates local FDR, q-value and FDRScore (http://onlinelibrary.wiley.com/doi/10.1002/pmic.200800473/abstract)
· Mzidentml2Csv - exports PSMs, proteins or protein groups to csv format.
· ProteoGrouper - performs protein inference on PSMs in mzIdentML files, outputting results in a new mzIdentML file containing ambiguity groups of proteins
· Thresholder - sets the passThreshold attribute on SpectrumIdentificationItem or ProteinDetectionHypothesis
MzidLib is a cross-platform utility capable of running on any operating system that comes with Java support (e.g. Mac OS X, Windows, Linux).