Big congrats to first authors Chau Ngo and Sho Takechi and a big thank you to all the authors and especially to our collaborators including @nesvilab.bsky.social @fcyucn.bsky.social @marcliesa.bsky.social and Ajit Divakaruni
Fengchao
@fcyucn.bsky.social
Research Investigator at U of M. Interested in proteomics, etc. Developer of FragPipe, MSFragger, IonQuant, etc.
Exited to share our latest work! Out now in @natcomms.nature.com Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA! www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
nature.com
This project started 5 years ago. It led us to add isotope-labeling support to #FragPipe/#IonQuant. Since then, the tools have grown so much and are now widely used in #Chemoproteomics. Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social
Stephan Hacker@stephanhacker2.bsky.social · 9mo agoHow can we study target engagement and selectivity of covalent inhibitors? Which electrophilic probes are best suited to study a certain amino acid? Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7) www.nature.com/articles/s41...
How can we study target engagement and selectivity of covalent inhibitors? Which electrophilic probes are best suited to study a certain amino acid? Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7) www.nature.com/articles/s41...
Profiling the proteome-wide selectivity of diverse electrophiles - Nature Chemistry
Covalent inhibitors are powerful entities in drug discovery. Now the amino acid selectivity and reactivity of a diverse electrophile library have been assessed proteome-wide using an unbiased workflow...
nature.com
Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline Presenters: Eduard Sabidó and Brendan MacLean When: Tuesday, September 16, 8am (Pacific Time) Register Now ... skyline.ms/project/home... #massspec #proteomics
Start Page: /home/software/Skyline/events/2025 Webinars/Webinar 26
skyline.ms
#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...
Nucleoside diphosphate kinase A (NME1) catalyses its own oligophosphorylation - Nature Chemistry
Our understanding of how post-translational modification—protein phosphorylation—impacts the complexity of eukaryotic signalling pathways is continuously expanding. Now, protein oligophosphorylation h...
nature.com
Interested in the proteome-wide selectivity of diverse electrophiles? The proteomics data for our study on this headed by @pzanon.bsky.social are now public on @pride-ebi.bsky.social: www.ebi.ac.uk/pride/archiv... Full story: chemrxiv.org/engage/chemr... #ChemBio #ChemSky #ChemicalProteomics
Profiling the proteome-wide selectivity of diverse electrophiles
Targeted covalent inhibitors are powerful entities in drug discovery, but their application has so far mainly been limited to addressing cysteine residues. The development of cysteine-directed covalen...
chemrxiv.org
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...
Don't tell PD, but I have quietly switched all of my analyses to Fragpipe. What an extremely powerful software. I'm often amazed at the sheer quantity of information I can get using Fragpipe. Thanks to everyone who recommended it.
Nicholas McCurtin, PhD 🧫 🏳️🌈@nicholasmccurtin.bsky.social · last yr.Extremely niche troubleshooting request, but is anyone familiar with implementing MSFragger in Proteome Discoverer? A few of us keep seeing these error messages, but none of us are tech savvy enough to decode it. Every time we "solve" it, it happens again.. #proteomics #teammassspec
Excited to be one of the guest editors! We’re calling for papers on cutting-edge #proteomics and #metabolomics in #multiomics research. Looking forward to your submissions!
Yasset Perez-Riverol@ypriverol.bsky.social · last yr.I'm co-editing a special issue at Genome Biology with @fcyucn.bsky.social: "Advances in Proteomics and Metabolomics." We're seeking innovative research that enhances the visibility and impact of #proteomics & #metabolomics in the context of #Multiomics. www.biomedcentral.com/collections/...
In addition to these exciting events, I’ll also be one of the panel members at the single-cell proteomics Evening Workshop on Wednesday. Looking forward to the discussions ahead!
Alexey Nesvizhskii@nesvilab.bsky.social · last yr.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
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”
Kusterlab@kusterlab.bsky.social · last yr.🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...
If there any #Sciex decision makers here on Bluesky - I urge you to reconsider. Skyline/Proteowizard support is not only important for your customers using these tools, but it also benefits other bioinformatics efforts that depend on these tools.
Chris Ashwood@cashwood.proteaglyco.com · last yr.Disappointing to see, across both parties. Sciex is no longer providing funding for Skyline/Proteowizard as part of the multi-vendor agreement to keep Skyline supported across all major vendors. I can see the arguments from both sides, just a shame it's resulted in this.
In this release, one of the major improvements is LFQ using IonQuant. Thanks to this excellent preprint (www.biorxiv.org/content/10.1...), we identified and fixed a suboptimal step in the XIC. We're always eager to listen to feedback from the community!
Alexey Nesvizhskii@nesvilab.bsky.social · last yr.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!
MSFragger-DDA+ is a database search tool that enhances peptide identification by searching the full isolation window. #Proteomics @fcyucn.bsky.social @nesvilab.bsky.social www.nature.com/articles/s41...
MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search - Nature Communications
Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...
nature.com
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...
MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search - Nature Communications
Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...
nature.com
One of the most significant and challenging projects of my career so far. PepCentric: a scalable computational platform utilizing novel 2-D fragment indexing for rapid peptide-centric searches, enabling proteogenomics searches against billions of spectra in seconds. www.biorxiv.org/content/10.1...
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...
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data - Nature Communications
Data-independent acquisition advances proteomics quantification. Here, the authors present diaTracer, a spectrum-centric tool for diaPASEF data that supports broad proteomics applications, enabling di...
nature.com
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data www.nature.com/artic... --- #proteomics #prot-paper
Looks interesting, and they already coupled it with MSFragger/FragPipe to search MS data using their fasta. I recommend using the group FDR option (available in FragPipe; requires annotating the headers in fasta in certain way) or a two-pass search option (canonical DB->unassigned mzML->custom DB).
Great to see them apply the proteome-wide profiling method for electrophile reactivity and selectivity that we developed together with @nesvilab.bsky.social in Fragpipe in this exciting system. chemrxiv.org/engage/chemr...
Profiling the proteome-wide selectivity of diverse electrophiles
Targeted covalent inhibitors are powerful entities in drug discovery, but their application has so far mainly been limited to addressing cysteine residues. The development of cysteine-directed covalen...
chemrxiv.org
