Good new histone publication from @jyates.bsky.social and colleagues
#FragPipe #Proteomics
www.biorxiv.org/content/10.6...
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#FragPipe
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Posts tagged #FragPipe
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🎓 Don’t miss our last training course of 2025!
Differential Proteomics Training
📍 Antwerp
📅 Dec 17, 2025 • 9:00 AM–noon
Learn to identify & quantify DDA/DIA proteomes using FragPipe & #FragPipe Analyst.
🔗 Details: www.denbi.de/training-cou...
#Proteomics #Bioinformatics #LCMSMS #ProteinAnalysis
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It was a great pleasure to teach #FragPipe at the Biological Proteomics for Beginners workshop at #UCSD, sponsored by Thermo Fisher Scientific. We had a fantastic group of grad students, postdocs, and professors. Yes, I even got to teach UCSD professors how to analyze bottom-up proteomics data 😁
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Wow, a record breaking number of the Nesvizhskii lab members attending #ASMS2025! 9 posters, 3 evening workshops, and one Bioinformatics Hub on #FragPipe. Plus multiple collaborative posters with other groups. See you in Baltimore! PS. Below is our recent group photo, including all those attending
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Yes, #FragPipe supports this, and we even have a paper describing it. link.springer.com/article/10.1...
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Great presentation on #FragPipe and its capabilities. Definitely learned a lot!
Thank you @nesvilab.bsky.social for virtually stopping by to give a talk during our #proteomics users group meeting here @stanford.edu and for answering all our questions 😊
#massspec
#teammassspec
#StanfordProteomics
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Has anyone used the glycopeptide and glycan unenriched template on a tribrid instrument? I am wondering if each fragmentation arm needs to be searched individually? EThcD for peptide and CID for glycan. Can #FragPipe do this?
#Glycoproteomics #Proteomics #TeamMassSpec
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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!
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DDA is still great for many applications, and #MSFragger-DDA+ improves peptide identification sensitivity via full isolation window search. Huge boosts in IDs, including Astral DDA! Fully integrated in #FragPipe, simply annotate your DDA files as DDA+ and RUN. www.nature.com/articles/s41...
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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.
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Plot of the day. 45,000 digly modified lysine residues (localization probability >0.75) in drug treated cells. #Proteomics #TeamMassSpec #FragPipe
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The next issue posted on our #FragPipe GitHub github.com/Nesvilab/Fra... will be #2000! Will it be a bug report or a feature request? From a new user or an expert FragPiper? About which of our workflows? Thanks to all users, and our team (especially @fcyucn.bsky.social) who respond to those issues.
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Sitting at Pike Place Market in Seattle at 7am in the morning, sipping coffee with my son, a long layover on the way home from Taipei. Otherwise I would do a long post. DiaTracer in #FragPipe work really well, making library-free analysis of any diaPASEF data possible. www.nature.com/articles/s41...
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#FragPipe has everything you need for any chemoproteomics data, including library free analysis or building hybrid libraries (if you have some DDA data).
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For our hands-on tutorials, or my University teaching (with ~ 50 students), we set up virtual windows servers (AWS), with #FragPipe installed. Several students can use one server. You can also use msconvert to extract a 10Th slice of the full file in mzML format; those can be run in parallel.
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MQ works sometimes... But mainly it's bugged AF. And the support ... As we're here very opensource minded, I'm waiting impatiently for the #fragpipe but we might also go into Biognosys solutions. Their software actually works and is fast. And I have many insiders in the tech support 😏
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