![]() ![]() ![]() It only includes results from 1 file of the 8 in the in the original mzidentML and doesn't seem to have the PS scores, just scores from individual engines. I've tried idconvert with PS 1.1.2 output and proteowiz, and the conversion finished with no errors, but the pepXML is rather useless. In my opinion, combining multiple search algorithms in PeptideShaker gives comprehensive results, better than Trans-Proteomic Pipeline and Proteome Discoverer, but it's very disappointing that the output is incompatible with other important data analysis tools, which were developed to accept the PeptideProphet output. Could you possibly provide a reliable parser for mzid that can emulate the peptideprophet pepxml output (and ProteinProphet if you really want to make my week)? Building a spectral library from DDA data and then using it for peptide-centric analysis of DIA data is a widely used workflow in the MS community. IDconvert in pPoteowizard produces an error when converting the PeptideShaker output and IDFileConverter, while able to convert the files, loses the spectrum reference information and the resulting pepXML file cannot be used to build a spectral library. However I am unable to convert the mzid output into a usable format for SpectraST, which takes PeptideProphet pepXML as input. ![]() Hi I'm attempting to use the output from PeptideShaker (after a SearchGUI data search) to generate a spectral library for Data Independent Acquisition (DIA) analysis. ![]()
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