🎓 Don’t miss our last training course of 2025!
Differential Proteomics Training
📍 University of Antwerp
📅 Dec 17, 2025 • 9:00 AM–noon
Learn to identify & quantify DDA/DIA proteomes using FragPipe & FragPipe Analyst. Get hands-on with LC-MS/MS data and discover how to detect differential protein expression in real datasets!
🔗 Details & preparation: https://www.denbi.de/training-courses-2025/2002-differential-proteomics-training
#Proteomics #Bioinformatics #deNBI #Antwerp #FragPipe #LCMSMS #ProteinAnalysis

Why is FragPipe/MSFragger always bailing out with a memory succession problem on the last slice of the main search - always at the very end.. unbelievable #fragpipe

How I do like the exporting of single CV tracks from Thermo .RAW files - when will DiaNN/FragPipe finally support multi-CV RAW files for DIA searches... #FragPipe #DIA #FAIMS

RT @nesvilab: Are you a #FragPipe user attending #HUPO2023 and have a question? Or just want to learn what’s new in MSFragger and other tools (DIA mode, Labile PTMs, MSBooster rescoring, wide window DDA etc). Talk to me, @fcyucn or @DanPolasky if you see us and come to our poster presentations

Anyone thought about forcing something like a flexible modification group in FragPipe - e.g., to have either dimethylation or acetylation on N-termini without constraints of having all as variable modifications for semi-specific searches? I am almost tempted to try dimethylation as fixed modification (e.g., + 28 Da)with variable mod for putative acetylations (+ 14 Da). #Proteomics #FragPipe

RT @: PTM-containing peptides often fragment in unexpected ways, hindering their identification. Here we describe a workflow in #FragPipe to find diagnostic spectral features for any PTM, illustrated using chemoproteomics, RNA-xlinks, glyco and ADP-ribo examples

Want to thank everyone here for some stellar discussion on SAAVs and searching.

Follow up: is there a SAAV-only open search option? So open-search but constrain fitting delta mass unknowns to AAs only (no funky ptms). I am off to poke around in #FragPipe but figured the crowd might know better.

#TeamMassSpec #teamProteome

https://fediscience.org/@neely/110666898318635047

RT @kalonji_08: Does anyone know how to Install #Fragpipe and all dependencies in Linux ? I’m having some #Java problem and I wouldn’t want to risk running it on my laptop. Please assist Thanks #massspec #Bioinformatics #proteomics

RT @nesvilab: Meet our #FragPipe team at #USHUPO23! We present our latest results on deep learning rescoring, HLA peptidomics, labile PTM searches, single cell proteomics (DIA,LFQ-MBR, TMT), plus two short courses. Find us, or contact me to schedule a meeting to discuss new collaborations etc.

A question for all the DiaNN experts here: I run DiaNN through FragPipe 19.1 and tried to see if there is a big deal in the "Unrelated runs" option in FragPipe for DiaNN. I totally understand the ID data differing, but not why the Total.Quantity if different for both run modi, though the MS1 and MS2 Quantities are identical?!? (in red the difference) #FragPipe #DiaNN

#TeamMassSpec
I use #FragPipe developed by the Nesvizhskii lab for #proteomics data analysis. The latest update has a link to analyze the results using a version of #LFQAnlyst compatible with FragPipe output called #FragPipe-Analyst.
http://fragpipe-analyst.nesvilab.org/
This is a powerful R statistical analysis workflow that anybody can quickly use to get descriptive and differential abundance results directly from the FragPipe output. Thanks @nesvilab