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Michael MacCoss @maccoss.bsky.social · 24d

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

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Fengchao @fcyucn.bsky.social · 29d

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 😁

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Alexey Nesvizhskii @nesvilab.bsky.social · Aug 20

#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

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Fengchao @fcyucn.bsky.social · Aug 14

Interesting idea. May I ask two questions?
1. Is the precursor detection performed before or after the database search?
2. If it is performed before the search, how can one identify the complementary fragment ions without knowing the precursor mass or peptide sequence?
Thanks

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Stephan Hacker @stephanhacker2.bsky.social · Aug 12

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

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Alexey Nesvizhskii @nesvilab.bsky.social · Aug 1

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...

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Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Jul 11

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.

Nick McCurtin (they/them) 🧫 🏳️‍🌈 @nicholasmccurtin.bsky.social · Apr 5

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

$System.IO.FileNotFoundException: Could not find file 'D:\nick (temporary local analysis folder)\HeLa Pulldown\HeLa Pulldown\temp1593\50nM_OspF_02.pepXML. File name: 'D:\nick (temporary local analysis folder)\HeLa Pulldown\HeLa Pulldown\temp1593\50nM_OspF_02.pepXML' at System.IO._Error.WinlOError(Int32 errorCode, String maybeFullPath) at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean FromProxy, Boolean useLongPath, Boolean checkHost) at System.IO.FileStream.ctor(String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize) at System.XmI.XmIDownloadManager.GetStream(Uri uri, Credentials credentials, IWebProxy proxy, RequestCachePolicy cachePolicy) at System.Xml.Xm|Ur|Resolver.GetEntityUri absoluteUri, String role, Type ofObject ToReturn) at System.Xml.Xm/TextReaderImpl.FinishInitUriString0 at System.Xml.XmIReaderSettings.CreateReader(String inputUri, Xm|ParserContext inputContext) at System.Xml.Xm|Reader.Create(String inputUri) at MSFraggerPDv30.PepXMLReader.ReadPepXML(String PepXMLPath)|$

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Fengchao @fcyucn.bsky.social · Jul 15

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 · Jul 15

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/...

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Fengchao @fcyucn.bsky.social · May 30

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 · May 30

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

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Alexey Nesvizhskii @nesvilab.bsky.social · May 30

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

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Alexey Nesvizhskii @nesvilab.bsky.social · May 23

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 · May 22

🚨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...

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

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Alexey Nesvizhskii @nesvilab.bsky.social · May 15

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 · May 13

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.

Transcribed text:
Skyline Targeted Mass Spec Environment

Dear Skyline Users,

I would like to thank Agilent, Bruker, Shimadzu, Thermo Fisher, and Waters for their continued funding support for the Skyline project this year. This industry/government/university partnership allows all of us to maximize the value of our efforts to provide better mass spectrometry tools to the field. In the current federal funding environment, industry support is critical to maintain our work.

Some instrument vendors, such as SCIEX, have not invested in the Skyline project this year. As a public university, we are limited in how we can support the private sector under state law. We paused our work in Skyline and ProteoWizard on support for SCIEX instruments to remain in compliance with state law. While we hoped SCIEX would resume its funding support of the Skyline project for use with their instruments, and respect their decision not to provide funding, we cannot continue our work to support SCIEX in Skyline or ProteoWizard without SCIEX funding. We have informed the ProteoWizard Foundation of this development.

As always, we look forward to seeing many of you at ASMS or our Skyline course at UW this summer. We thank all of you for your continued support.

Brendan MacLean,

Skyline Project Lead

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Fengchao @fcyucn.bsky.social · May 8

We didn’t cherry-pick the dataset for the benchmark—FragPipe also delivers excellent performance on another dataset (PXD028735).

Questions are always welcome! We're always happy to hear your feedback. (3/3)

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Fengchao @fcyucn.bsky.social · May 8

Peptide-level LFQbench-style plot using the PXD003881 (IonStar) dataset. (2/3)

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Fengchao @fcyucn.bsky.social · May 8

We also benchmarked LFQ precision and accuracy against the latest versions of other popular tools. Here's an protein-level LFQbench-style plot using the PXD003881 (IonStar) dataset. (1/3)

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Fengchao @fcyucn.bsky.social · May 7

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!

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Qian Cheng @qchengx1e3.bsky.social · Apr 15

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...

www.nature.com

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Alexey Nesvizhskii @nesvilab.bsky.social · Apr 9

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

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Fengchao @fcyucn.bsky.social · Mar 4

Feature request well received🫡

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Alexey Nesvizhskii @nesvilab.bsky.social · Mar 4

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...

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Fengchao @fcyucn.bsky.social · Jan 4

It doesn't "predict" the library. It perform the spectrum-centric search to get the IDs and build the experimental library.

And for the DIA without ion mobility, it is basically what DIA-Umpire is doing: www.nature.com/articles/nme...

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics - Nature Methods

The computational workflow of DIA-Umpire allows untargeted peptide identificationdirectly from DIA (data-independent acquisition) proteomics data without dependence on a spectral library for data extr...

www.nature.com

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Alexey Nesvizhskii @nesvilab.bsky.social · Jan 4

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

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Fengchao @fcyucn.bsky.social · Jan 4

Perfect timing: 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

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PastelBio @pastelbio.bsky.social · Jan 3

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data www.nature.com/artic...

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#proteomics #prot-paper

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Fengchao @fcyucn.bsky.social · Jan 4

Mostly, yes, AFAIK. The Gaussian feature detection was also inspired by Alexey's previous work doi.org/10.1021/acs.... Although that work was for top-down but we found that the ion mobility shapes were similar to timsTOF's.

IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry

Top-down proteomics has emerged as a transformative method for the analysis of protein sequence and post-translational modifications (PTMs). Top-down experiments have historically been performed prima...

doi.org

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