FragPipe users: I've updated PSManalyst shiny app. Check it out and enjoy the easiest way to evaluate the quality of your runs. Now you can map peptides to protein coverage counting PSMs.
github.com/41ison/PSMan...

A Chemical Proteomics Method to Quantify Cysteine S-Acylation S-acylation, often referred to as S-palmitoylation, is a reversible and dynamic posttranslational modification that corresponds to the addition of a long-chain fatty acid to cysteine (Cys) residues. Established mass spectrometry-based chemoproteomics methods have improved our understanding of the S-acylation proteome, notably by identifying hundreds of S-acylated proteins, sometimes with the modified Cys. However, the precise quantification of S-acylation levels for each Cys within a single sample remains challenging at the proteome level. Quantification of S-acylation levels is critical to further our understanding of protein S-acylation in cellular function and its role in health and diseases. We report here the development of an S-acylation quantification workflow based on the sequential labeling of free Cys and S-acylated Cys with isotopic labeling reagents. The workflow was extensively optimized, notably by comparing the number of sites identified with two alkyne-tagged Cys-reactive isotopic probes and four azido-tagged biotin-based capture reagents. By integrating this enhanced workflow with high-field asymmetric waveform ion mobility spectrometry (FAIMS) on LC–MS/MS instruments for the separation of labeled peptides, over 17,000 unique Cys could be quantified in biological samples. Application of the S-acylation quantification workflow to cellular proteomes allowed for the quantification of S-acylation levels in a HeLa proteome. We also identified dynamic S-acylation changes in response to autophagy induction.

A Chemical Proteomics Method to Quantify Cysteine S-Acylation | ACS Chemical Biology pubs.acs.org/doi/abs/10.1...

Good new histone publication from @jyates.bsky.social and colleagues

#FragPipe #Proteomics

www.biorxiv.org/content/10.6...

The May Institute, if you don't know, combines the full workup of generating mass spec proteomics data all the way to doing the statistics.

This year has a few new modules, like FragPipe with @nesvilab.bsky.social and @fcyucn.bsky.social, so even if you've attended in the past, check it out!

A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs pubs.acs.org/doi/10....

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#proteomics #prot-paper

So glad to see this online today! With FragPipe and the many other Koina APIs, we wanted to democratize deep learning, especially for those without access to expensive GPUs. Major kudos to my co first author Ludwig for setting up the server. I encourage ML developers to put their models on Koina

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...

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...

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

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...

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...

This work led by Elena Levi-D'Ancona, a recent PhD graduate in our lab, was our first cover and only possible due to our amazing team and outstanding collaborators, including @nesvilab.bsky.social and Orian Shirihai, and funding from NIDDK, Breakthrough T1D, and the VA! Thank you! 🤗🙌 2/fin

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

exact quote is "this site is being blocked due to DOJ Bulk Sensitive Data Regulations as the site is hosted in a Geo-Fenced country". I think replication of the data would be the only option for us in the foreseeable future.

The University of Michigan now blocks the iProX database, which is a part of the PRIDE consortium of mass spec data repositories. All requests to unblock were denied. Any other US universities in a similar situation? There is a lot of valuable MS proteomics data there no longer accessible to us.

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 😁

Peptide-RNA photo-crosslinks with tunable RNA chain map protein-RNA interfaces Photo-crosslinking mass spectrometry enables the identification of protein-RNA interactions in living cells, pinpointing interaction interfaces at single-amino acid resolution. However, current isolat...

New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...

Dan Polasky is indeed a perfect teammate, and not only in our lab but also apparently as a … player in Kubb. I also want to use this opportunity to publicly congratulate Dan for being promoted to Research Assistant Professor starting September 1st!

Crystal-C: A Computational Tool for Refinement of Open Search Results Shotgun proteomics using liquid chromatography coupled to mass spectrometry (LC-MS) is commonly used to identify peptides containing post-translational modifications. With the emergence of fast databa...

I am not going to answer for “the field” but - in our tools - the short answer is yes. From introducing localization-aware open search, to Crystal-C artifact removal pubs.acs.org/doi/10.1021/..., to PTM-Shepherd summarization and visualization tools, we provide guardrails if not guidelines.

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...

#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...

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results FragPipe is recognized as one of the fastest computational platforms in proteomics, making it a practical solution for the rapid quality control of high-throughput sample analyses. Starting with version 23.0, FragPipe introduced the “Generate Summary Report” feature, offering .pdf reports with essential quality control metrics to address the challenge of intuitively assessing large-scale proteomics data. While traditional spreadsheet formats (e.g., tsv files) are accessible, the complexity of the data often limits user-friendly interpretation. To further enhance accessibility, PSManalyst, a Shiny-based R application, was developed to process FragPipe output files (psm.tsv, protein.tsv, and combined_protein.tsv) and provide interactive, code-free data visualization. Users can filter peptide-spectrum matches (PSMs) by quality scores, visualize protease cleavage fingerprints as heatmaps and SeqLogos, and access a range of quality control metrics and representations such as peptide length distributions, ion densities, mass errors, and wordclouds for overrepresented peptides. The tool facilitates seamless switching between PSM and protein data visualization, offering insights into protein abundance discrepancies, samplewise similarity metrics, protein coverage, and contaminants evaluation. PSManalyst leverages several R libraries (lsa, vegan, ggfortify, ggseqlogo, wordcloud2, tidyverse, ggpointdensity, and plotly) and runs on Windows, MacOS, and Linux, requiring only a local R setup and an IDE. The app is available at (https://github.com/41ison/PSManalyst.

It's now properly published. If you want to easily check important characteristics of your data before diving into complicated statistics, check out PSManalyst.

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

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...

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

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...

Have you compared FragPipe on i9 vs comparably priced AMD threadripper? I put a request to our IT to get me one but they do not support core imaging of AMD machines. I am still recommending a good Xeon or i9 to folks who want a standard desktop to run FragPipe on a < $5k machine but want to test AMD

LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes - Nature Metabolism LONP1, whose expression is downregulated in islets from donors with type 2 diabetes, is vital to mediate efficient mitochondrial protein folding, thus preventing proteotoxicity and promoting islet β c...

Type 2 diabetes is often considered a protein misfolding disease. But where are these toxic proteins found? 🤔

🚨In new work out today in @natmetabolism.nature.com, we show that mitochondrial protein misfolding (yes mitos🤯) leads to beta cell damage in T2D. 🚨 nature.com/articles/s42... 1/n

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.

GitHub - pwilmart/quantitative_proteomics_comparison: Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies - pwilmart/quantitative_proteomics_comparison

DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before:
github.com/pwilmart/qua...

I miss Twitter a bit. With its outrageous commercials and all those gorgeously looking “Lucy564” people who seemed to wanted to follow me in droves. Ok, not really. I do occasionally check Bluesky but I only see posts from a few (mostly same) people. Lack of critical mass?

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”

Targeted proteomics: Advanced tools for biomedical research Targeted proteomics technologies, and specially data-independent acquisition techniques, have revolutionized the landscape of proteomic research in the last decade offering researchers unprecedented …

Don't miss out! Applications still open for EMBO Practical Course on Targeted proteomics: Advanced tools for biomedical research in Barcelona, Spain, 5 – 10 October 2025

Abstract submission & registration deadline: 15 May

meetings.embo.org/event/25-tar...
#EMBOtargetedProteomics #EMBOevents 🧪

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.