5 years ago this project kicked off and sparked isotope-labeling support in #FragPipe / #IonQuant. Today, these tools are widely used across #Chemoproteomics. Huge thanks to all contributors, esp. @StephanHacker2 & @patrick_zanon!

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 do proteomics 😁

Conventional proteomics searches struggle with many modifications and open searches may be difficult to interpret. We introduce a "detailed" mass offset search in #MSFragger boosting interpretability and localization especially in complex cases like FPOP: https://t.co/JeqUNAjrwO

The Nesvizhskii lab has 9 members attending #ASMS2025! 9 posters, contribution to 4 evening workshops, and one Bioinformatics Hub on #FragPipe. Plus multiple collaborative posters with other groups. See you in Baltimore!

MSFragger-DDA+ is a database search tool that enhances peptide identification by searching the full isolation window. #Proteomics @fcyucn @nesvilab #BiotechNatureComms https://t.co/bBFLMlQlyl

DDA is still great for many applications, and #MSFragger-DDA+ improves peptide identification rates 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.

Tim Griffin, @nesvilab and Bing Zhang, will have a panel discussion on 'MS-Based #Immunopeptidomics: Challenges and Opportunities in Immuno-Oncology Research' at the #USHUPO2025 conference on 23rd Feb.

Our #diaTracer manuscript is out! 10 years ago we established the concept of library-free, direct DIA analysis with DIA-Umpire. DiaTracer now makes it possible to analyze any diaPASEF data, including PTM, semi-tryptic, nonspecific, and even open searches!

.@KaiPeiLi @nesvilab @fcyucn present diaTracer, a spectrum-centric tool for diaPASEF data, enabling direct peptide identification and quantification without spectral libraries. #BiotechNatureComms https://t.co/pLTEUyyjwb

Spent a great day in Barcelona at the EMBO Targeted Proteomics course hosted by @sabidolab, talking about our DIA tools and helping his team with a hands-on tutorial on FragPipe, FragPipe-Analyst, and Skyline integration, from installation and mzML files to pathway-level results.

Very nice paper in Science, showing that N-glycosylation can also function as a degradation signal, similar to Ubiq: https://t.co/O39BA5RcEa. Glad to see the authors used our #FragPipe/#MSFragger-Glyco “Glyco-N-LFQ” workflow for quantitative glycoproteomics data analysis.

Another great collaboration with the Keri Backus' lab, where we implemented a two stage search in #FragPipe to identify gain-of-cys mutations and variants proximal to reference cysteines. Two-stage searches can be useful for many applications, and they ensure group-specific FDR.

@NatureComms @heta_desai17 This was a really fun collaboration with @nesvilab and @fcyucn applying a two stage FDR search in FragPipe to identify gain-of-cys mutations and variants proximal to reference cysteines

Excited to share our chemoproteogenomics story now out in its final form in @NatureComms. Congrats to first author Heta Desai @heta_desai17!

Kevin Yang from the @nesvilab closing the data analytics session by showing the power of MSFragger for scp-MS - incredible what free, academic software can do! #iSCMS2024

@mjmaccoss @wfondrie @paragmallick Some commercial companies do not even offer evaluation licenses or can refuse one. When our MSFragger-Glyco manuscript was under review, one reviewer asked us to compare with Byonics. We contacted the company. They asked me about the purpose of me getting a license, and refused.

@wfondrie I agree with many points, but there is one problem. The commercialization of mass spec tools via spin-off has resulted in the loss of free access to academics (e.g. Byonics, PEAKS, Spectronaut). I am adamant about our tools free for academics, and searching for ways to do that.

@wfondrie My second point is the timing of the source code release. When the software is being actively developed and research is still ongoing, the scientists should have the right to protect their work and their IP, especially when there is a direct competition with commercial companies.

@wfondrie Third, it is possible to implement your innovation in a closed source code AND do it in a transparent, reproducible way. Evidence: almost identical reimplementation of our MSFragger method by others. Plus, downstream FDR analysis (MSBooster, Percolator Philosopher) is open source

I had to shorten my trip to Dresden for #HUPO2024 and have a room for Friday and Saturday night, and the following Wednesday night, that will sit empty. They require 14 day cancelation notice. If anyone in a desperate need for a place to stay on those nights, email me.