de.NBI & ELIXIR GermanyDec 16
🎓 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
Fatih DemirNov 7, 2024
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
Fatih DemirOct 4, 2023
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
PastelBioSep 17, 2023
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
Fatih DemirSep 14, 2023
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
PastelBioJul 12, 2023
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
Ben NeelyJul 7, 2023

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

Ben Neely (@[email protected])

@[email protected] was talking about protein variants in blood, and I don’t know why, but I had never thought about how to make a fasta of variants. I can almost see how to do it, but how to deal with multiple variants on a tryptic peptide (assuming all combinations)… but yeah, any clever ideas before I brute force this? Or better yet, a favorite protein with observable variants to test with?

FediScience.org
PastelBioMar 7, 2023
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
PastelBioMar 1, 2023
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.
Fatih DemirJan 16, 2023
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