MSFragger
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Nesvilab
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
Dear MSFragger developing team, Thank you again for this amazing software. We are making good progress with using the none-specific HLA workflow in MSFragger. Our collaborator is interested to do...
I've run a couple of searches with MSFragger - Glyco, and I have noticed that it only identifies one glycosylation site (despide increasing the number of possible modifications). Is there...
Hi, AFAICT, MSFragger has no built-in way of addressing known single amino acid polymorphisms ([cf. x!tandem](https://thegpm.org/TANDEM/api/rsaps.html)). Is such an option on the agenda and/or it there a good workaround recommendation?...
Add support for different modifications ontologies and make it possible to define modifications names on the parameter file.
Why am I getting insufficient memory error in Fragpipe (though I have enough memory, it is not using it fully)?
Hi, I'm interested in using the Labile search mode in MSFragger, but the tutorials mainly focus on high-resolution MS data. Could you please give some advice on setting validation and...
Hello, I am interested in getting lists of of matched ions for each PSM as part of the search results. For example, something like: ``` matched_y_ions="y1+=175.118952913371, y3+=361.18301123237103, etc...", matched_b_ions="..." ```...
Hi Fragpipe developers, I'm trying to do a protein ID and LFQ of 12 samples using Fragpipe on the CLI, just like many times before. I ran into this issue...
To preserve Waters and Sciex source spectrum links, writing nativeID in the output pepXML/mzIdentML is necessary. Please read in the nativeID when reading spectra and pass it through when writing...
Hello Fragpipe team, I am trying to analyze results from a mass-offset search. In the psm.tsv output, there are some PSMs with a reported 'Modified Peptide' but no 'Assigned Modification'....
