Chris McGann

US HUPO - Distinguished Contribution Award

Congratulations to Mike MacCoss on receiving the Donald F. Hunt Distinguished Contribution in Proteomics Award from US HUPO!
us-hupo.org/Distinguishe...

US HUPO - Computational Proteomics Award

Congratulations to Bill Noble on receiving the 2026 Gil Omenn Computational Proteomics Award from US HUPO!
us-hupo.org/Computationa...

If you’re at #HUPO2025, be sure to stop by my poster and learn about the latest developments in the BioPlex project!

More #gastruloid studies. Benchmarking correlations between RNA/proteins w/ acquiring information @ phosphorylation across #mouse & #human www.biorxiv.org/content/10.1...
Also looking at #Disease modelling. Fantastic #TourDForce Valuable bench marking and insight
@dschweppe.bsky.social #SCBEMs

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...

Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...

Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

Excited to see this published in JPR. For years I've wanted a simple way to standardize the signal between instruments. We use the precision of an intraspectrum ratio to assess the relationship between the reported signal and the number of ions. pubs.acs.org/doi/10.1021/...

Can nanoparticles help us probe the glycoproteome?

The new pre-print from @riley-research.bsky.social seeks to answer this question using the Proteograph technology from Seer Inc.

Check out this lovely study on glycoproteins NP-enriched from biofluids here: chemrxiv.org/engage/chemr...

Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface Applications using real-time spectral analysis and real-time instrument control have emerged in recent years as powerful tools to improve the capabilities and sensitivity of mass spectrometers. Softwa...

pubs.acs.org/doi/10.1021/...

Real-time API control of mass specs has been hard to get started (C#, VS, etc). Mike Hoopmann's recent work makes dev easier & more open!:

Nova - lightweight dev library
schweppelab.github.io/Nova/ pubs.acs.org/doi/full/10....

Helios - a unified instrument API now @ JPR
github.com/SchweppeLab/...

Thanks William!

Thanks!! I’m back to Boston for a postdoc!

After five great years, my journey in the Schweppe Lab and at UW has come to a close. Huge thanks to @dschweppe.bsky.social and all the amazing labmates for making graduate school such a wonderful experience. Extremely grateful for the memories and all the help I received along the way.

[ASAP] Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00110

(JASMS) [ASAP] Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00110 (RSS) #MassSpecRSS #JASMS

News in Proteomics Research blog post | Nova! Build all the mass spec tools! proteomicsnews.blogs...



---
#proteomics #prot-other

Thousands of forms, one protein: how Tim Veth is deciphering the complex language of Glycans Tim Veth, a postdoctoral researcher working with Prof. Nicholas M.

"I invite all researchers to enter the glycoproteomics field and join the battle.”

With the complexity of glycoproteomics and how little we still know, Tim Veth puts out a rallying cry to speed up development in this promising field.

Learn more about Tim & read our discussion: bit.ly/3IXpo8B

Nova: A Library for Rapid Development of Mass Spectrometry Software Applications pubs.acs.org/doi/10....

---
#proteomics #prot-paper

The yEvo Mutation Browser: Enhancing student understanding of experimental evolution and genomics through interactive data visualization Experimental evolution is a powerful method for studying the relationship between genotype and phenotype by observing how populations genetically adapt to controlled selective pressures. In educationa...

Announcing the yEvo Mutation Browser, a Shiny app for visualizing and exploring sequencing data from experimental evolution and genetic screens. This is the latest from our @yevolab.bsky.social high school teaching & research project and led by my grad student Leah. www.biorxiv.org/content/10.1...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

If you asked me 5 years ago if it would be possible to use a de novo tool on DIA data, I would have thought it would only exist in science fiction. Love being proved wrong. Great work from Justin Sanders. #proteomics #massspectrometry
www.nature.com/articles/s41...

Thanks so much @dschweppe.bsky.social!!! Couldn’t ask for a better place to do graduate school than the Schweppe Lab!

Huge congratulations to @chrismcgann.bsky.social who passed his PhD dissertation defense yesterday with flying colors!!

Dr. McGann was the lab’s first PhD student and now first graduate! So excited and proud of all of the things he’s accomplished!

Comet's open-source Fragment-Ion Indexing work is live at JPR (@acs.org). @chrismcgann.bsky.social, Jimmy Eng and Erik Bergstrom showed how Comet could be dramatically sped up to keep pace with modern instrumentation and increasing sample sizes:
pubs.acs.org/doi/full/10....

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...

Assessing error control is fundamental in mass spectrometry-based proteomics. @bo-wen.bsky.social @maccoss.bsky.social @urikeich.bsky.social et al introduce a theoretical foundation for entrapment along with a method for more accurate evaluation of FDR control.
www.nature.com/articles/s41...

Congrats to @chrismcgann.bsky.social (and the other awardees) for receiving an @asms.org Graduate Student Travel Award!!

Photo credit to Katarina for capturing the moment!

Thanks to everyone who came out to the Real time MS bioinformatics hub yesterday! Great to chat about current and new directions! Here’s some action shots of Mathieu and Mike leading the discussion.

#ASMS2025 offers great evening workshops. If you are interested in real-time decision-making during MS data acquisition or still looking for one to join,

consider the Real time Mass Spectrometry Workshop featuring speakers and panelists Sarah Sipe, Aarthie Senathirajah, and Manuel Peris Diaz.

Nova: A library for rapid development of mass spectrometry software applications www.biorxiv.org/cont...

---
#proteomics #prot-preprint

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data A core computational challenge in the analysis of mass spectrometry data is the de novo sequencing problem, in which the generating amino acid sequence is inferred directly from an observed fragmentat...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data
www.biorxiv.org/content/10.1...

impressive work!

Molecular Phenotyping With Proteomics This JAMA Insights explores the capability of proteomics to analyze thousands of proteins in patient samples, which could improve clinicians’ understanding of and ability to treat a wide range of dise...

This JAMA Insights explores the capability of proteomics to analyze thousands of proteins in patient samples, which could improve clinicians’ understanding of and ability to treat a wide range of diseases.

ja.ma/4jvNHbP

#MedSky

This prototype 908 devices SPE-CZE column and emitter combination looks to be the separation method to beat for localising phosphosites on multiply phosphorylated peptides.