Hello everyone,

I started using the Bioconductor package for R 3.6 (BiocManger). I want to use the package MSGFplus to identify proteins from mass spectrometer data (.mzXML) and to do so you can specify parameter for the search via msgfPar(). One parameter defines the enzyme which was used to digest the proteins. Here comes my question. Is it possible to specify more than one protein which was used for digestion?

this is my current code: msgfpar <- msgfPar(database = filePathToFastaFile, instrument = 'HighRes', tda = TRUE, enzyme = 'Trypsin', protocol = 0) idres <- runMSGF(msgfpar, filePathTomzXMLFile, memory=10000)

Any help is appreciated :) Cheerio

https://msgfplus.github.io/msgfplus/MSGFPlus.html No, this is not possible. Here is a workaround. Set specificity to "0: Unspecific cleavage" or whatever the right way setting this parameter would be in this package. Then deal with cleavage specificity later.