Latest posts tagged with #MSFragger on Bluesky
We established a completely unbiased workflow to study electrophile reactivity and selectivity in the entire proteome using isoDTB-ABPP (onlinelibrary.wiley.com/doi/full/10....) and analysis in #MSFragger (www.nature.com/articles/nme...) and applied it to characterize >50 electrophiles. (2/7)
#MSFragger Open Search has been around for a while now and used by mass spec folks to screen for chemical artifacts and adducts, e.g. in chemoproteomics data. Happy to see it got 'discovered' by a broader community who are now reporting all sort of cool biological PTMs www.nature.com/articles/s41...
Conventional proteomics searches struggle with many modifications and fully open searches may be difficult to interpret. We introduce a "detailed" mass offset search in #MSFragger boosting interpretability and localization especially in complex cases (e.g. FPOP data): www.biorxiv.org/content/10.1...
The power of #MSFragger open search! “we applied the mass-tolerant search engine MSfragger and found that phosphorylation as well as ubiquitination were well preserved after XDNAX. To our great interest, we found an additional modification of 321 Da occurring only in the irradiated SILAC channel”
Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!
This is why everyone should run open searches and semi-tryptic searches on their samples, at least once in a while (and may I suggest a tool for that, #MSFragger in #FragPipe). I do it all the time myself as a “hobby”, using already published data, and find so many weird and interesting things.
