WeĪre also working on the combination with DIA Umpire, so with the support of Make our tools compatible, so we might be able to bypass the problem. On a more positive note, I have been in contact with OpenSWATH people to I am not sure to whichĮxtend we can fix it but I can try to look into it if I get some time. Put the information we have in PeptideShaker, so in the end you might evenĮnd up not being able to use this file at all. This is typically poorlyĭocumented if documented at all, so supporting and maintaining theseĮxports is a very time consuming task. The specific flavour expected by a given pipeline. Uncovering why we don't support pepXML: depending on the tool every pepXMLįile is different, so we basically not only need to write pepXML but write Thanks for all these details it is very instructive. Just thought I'd ask again, as I do really like the software, but can't use it in my workflows due to these compatibility issues. Although it's good news that they're now able to import mzidentML. I need to make a traML iRT calibrated spectral library, using an OpenSWATH + SpectraST pipeline, and switching between spectral library formats is even more difficult than identification files, so Skyline will not help there. Unfortunately my group is not very strong in the programming department so we cannot contribute. So I've reached a bit of a dead end in that direction as well. As I'm sure you are aware, it's not easy getting developers to adjust their input and output formats. As I mentioned, the OpenMS (IDFileConverter) solution works for some applications, but in this case the spectrum information was removed from the pepXML so it is not suitable for building a spectral library. 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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