Lightnews — Scholar-powered news

Reposted by Chris McGann

Emmajay Sutherland @emmajays.bsky.social · 15d

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...

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Reposted by Chris McGann

Mike Goodwin @massspecpro.bsky.social · 25d

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

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

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Reposted by Chris McGann

Devin Schweppe @dschweppe.bsky.social · Sep 8

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/...

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Chris McGann @chrismcgann.bsky.social · Sep 6

Thanks William!

Chris McGann @chrismcgann.bsky.social · Sep 6

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

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Chris McGann @chrismcgann.bsky.social · Sep 5

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.

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Reposted by Chris McGann

Kermit Murray @kkmurray.bsky.social · Aug 9

(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

[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

dlvr.it

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Reposted by Chris McGann

PastelBio @pastelbio.bsky.social · Jul 24

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

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#proteomics #prot-other

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Reposted by Chris McGann

IonOpticks @ionopticks.bsky.social · Jul 23

"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

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.

bit.ly

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Reposted by Chris McGann

PastelBio @pastelbio.bsky.social · Jul 22

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

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#proteomics #prot-paper

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Maitreya Dunham @maitreya.bsky.social · Jul 22

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...

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...

www.biorxiv.org

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Reposted by Chris McGann

Michael MacCoss @maccoss.bsky.social · Jul 2

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...

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...

www.nature.com

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Chris McGann @chrismcgann.bsky.social · Jun 26

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

Devin Schweppe @dschweppe.bsky.social · Jun 26

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!

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Reposted by Chris McGann

Devin Schweppe @dschweppe.bsky.social · Jun 26

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!

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Reposted by Chris McGann

Devin Schweppe @dschweppe.bsky.social · Jun 17

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....

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Reposted by Chris McGann

Nature Methods @natmethods.nature.com · Jun 16

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...

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...

www.nature.com

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Reposted by Chris McGann

Devin Schweppe @dschweppe.bsky.social · Jun 4

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!

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Reposted by Chris McGann

Devin Schweppe @dschweppe.bsky.social · Jun 3

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.

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Reposted by Chris McGann

Nick Riley @nmriley.bsky.social · Jun 2

#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.

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Reposted by Chris McGann

PastelBio @pastelbio.bsky.social · May 12

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

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#proteomics #prot-preprint

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Reposted by Chris McGann

UW Genome Sciences @uwgenome.bsky.social · Apr 22

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

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...

www.biorxiv.org

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Chris McGann @chrismcgann.bsky.social · Mar 3

impressive work!

PastelBio @pastelbio.bsky.social · Mar 3

Affinity Purification Mass Spectrometry on the Orbitrap–Astral Mass Spectrometer Enables High-Throughput Protein–Protein Interaction Mapping pubs.acs.org/doi/10....

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#proteomics #prot-paper

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Reposted by Chris McGann

JAMA @jama.com · Jan 30

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

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...

ja.ma

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Reposted by Chris McGann

Chris Ashwood @cashwood.proteaglyco.com · Dec 13

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.

A plot demonstrating SPE-CZE outperforms nano-LC for localising phosphorylation sites

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Reposted by Chris McGann

bioRxiv SysBio @biorxiv-sysbio.bsky.social · Dec 13

SPE-CZE-MS quantifies zeptomole concentrations ofphosphorylated peptides https://www.biorxiv.org/content/10.1101/2024.12.07.627347v1

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