Fengchao
@fcyucn.bsky.social
Research Investigator at U of M. Interested in proteomics, etc. Developer of FragPipe, MSFragger, IonQuant, etc.
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
Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social
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...
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...
www.nature.com
October 30, 2025 at 2:15 PM
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
Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social
Reposted by Fengchao
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...
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...
www.nature.com
October 30, 2025 at 10:27 AM
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...
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Reposted by Fengchao
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
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
September 15, 2025 at 8:26 AM
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
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
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 😁
September 10, 2025 at 2:52 PM
Reposted by Fengchao
#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...
www.nature.com
August 20, 2025 at 3:55 PM
#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...
Reposted by Fengchao
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
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
August 12, 2025 at 9:50 AM
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
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
Reposted by Fengchao
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...
August 1, 2025 at 9:33 PM
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...
Reposted by Fengchao
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.
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
July 11, 2025 at 8:49 PM
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.
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!
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/...
July 15, 2025 at 6:21 AM
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!
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!
May 30, 2025 at 9:42 PM
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!
Reposted by Fengchao
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
May 30, 2025 at 7:45 PM
Reposted by Fengchao
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”
🚨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...
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...
The human proteome with direct physical access to DNA
Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living
cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale
of minutes with single-amino-aci...
www.cell.com
May 23, 2025 at 12:41 PM
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”
Reposted by Fengchao
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.
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.
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.
May 15, 2025 at 1:24 AM
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.
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!
May 7, 2025 at 11:40 PM
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!
Reposted by Fengchao
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...
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...
www.nature.com
April 15, 2025 at 4:39 PM
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...
www.nature.com/articles/s41...
Reposted by Fengchao
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...
www.nature.com
April 9, 2025 at 1:27 PM
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...
Reposted by Fengchao
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...
March 4, 2025 at 9:09 AM
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...
Reposted by Fengchao
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...
www.nature.com
January 4, 2025 at 4:04 PM
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...
Reposted by Fengchao
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
January 3, 2025 at 5:20 PM
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
Reposted by Fengchao
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).
December 10, 2024 at 5:31 PM
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).
Reposted by Fengchao
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
November 21, 2024 at 9:28 AM
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...
Reposted by Fengchao
Apparently FragPipe is updating! #proteomics
December 21, 2023 at 5:22 PM
Apparently FragPipe is updating! #proteomics