Michael MacCoss
@maccoss.bsky.social
Professor of Genome Sciences University of Washington, Seattle. Interested in proteomics and mass spectrometry.
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...
www.nature.com/articles/s41...
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...
www.nature.com
November 6, 2025 at 3:49 PM
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...
www.nature.com/articles/s41...
Reposted by Michael MacCoss
My favourite attendee feedback:
"I loved this class and I am super excited about Skyline, which is totally new to me. Halfway into the class I'm thinking "I've been living under a rock, this is going to change my life!" Without a doubt this class will have the highest ROI of anything I do this year"
"I loved this class and I am super excited about Skyline, which is totally new to me. Halfway into the class I'm thinking "I've been living under a rock, this is going to change my life!" Without a doubt this class will have the highest ROI of anything I do this year"
Wrapping up the 2025 Skyline Online Small Molecule course! Fantastic instructors and presenters, including Haley from the Baker lab with an insightful ion mobility crash course.
Great discussion and interaction from participants this year—looking forward to next year! #teammassspec
Great discussion and interaction from participants this year—looking forward to next year! #teammassspec
November 5, 2025 at 11:55 AM
My favourite attendee feedback:
"I loved this class and I am super excited about Skyline, which is totally new to me. Halfway into the class I'm thinking "I've been living under a rock, this is going to change my life!" Without a doubt this class will have the highest ROI of anything I do this year"
"I loved this class and I am super excited about Skyline, which is totally new to me. Halfway into the class I'm thinking "I've been living under a rock, this is going to change my life!" Without a doubt this class will have the highest ROI of anything I do this year"
Reposted by Michael MacCoss
Day 1 of the @asms.org Fall Workshop on "Fundamentals of Instrumentation" and oh boy I am humbled.
www.asms.org/conferences/...
www.asms.org/conferences/...
Fall Workshop Homepage
www.asms.org
November 3, 2025 at 5:32 PM
Day 1 of the @asms.org Fall Workshop on "Fundamentals of Instrumentation" and oh boy I am humbled.
www.asms.org/conferences/...
www.asms.org/conferences/...
Reposted by Michael MacCoss
Understanding m/z range settings for MS/MS scans: a case study with intact glycopeptides chemrxiv.org/engage/...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
October 22, 2025 at 6:40 PM
Understanding m/z range settings for MS/MS scans: a case study with intact glycopeptides chemrxiv.org/engage/...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
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/...
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...
pubs.acs.org
October 22, 2025 at 3:32 PM
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/...
Reposted by Michael MacCoss
Wrapping up the skyline.ms virtual workshop on #MassSpectrometry #proteomics with Advanced Proteomics: data independent acquisition today, post-translational modifications tomorrow. @juank1892.bsky.social @arianashannon.bsky.social @miriamabele.bsky.social (anybody else on bsky?) 🖥️🧬🧪
October 16, 2025 at 3:22 PM
Wrapping up the skyline.ms virtual workshop on #MassSpectrometry #proteomics with Advanced Proteomics: data independent acquisition today, post-translational modifications tomorrow. @juank1892.bsky.social @arianashannon.bsky.social @miriamabele.bsky.social (anybody else on bsky?) 🖥️🧬🧪
Reposted by Michael MacCoss
Lost Science is a new NYT series of accounts from scientists who have lost their jobs or funding. You can send your story to the Times here www.nytimes.com/2025/10/08/c...
October 10, 2025 at 8:38 AM
Lost Science is a new NYT series of accounts from scientists who have lost their jobs or funding. You can send your story to the Times here www.nytimes.com/2025/10/08/c...
Reposted by Michael MacCoss
Very excited to kick off the annual Skyline Online 2025 Small Molecule course with a keynote lecture by Gary Patti @gjpattij.bsky.social.
Showing how his lab and collaborators are advancing mass spectrometry to achieve parity with sequencing techs, supported by Skyline!
Showing how his lab and collaborators are advancing mass spectrometry to achieve parity with sequencing techs, supported by Skyline!
October 8, 2025 at 1:57 PM
Very excited to kick off the annual Skyline Online 2025 Small Molecule course with a keynote lecture by Gary Patti @gjpattij.bsky.social.
Showing how his lab and collaborators are advancing mass spectrometry to achieve parity with sequencing techs, supported by Skyline!
Showing how his lab and collaborators are advancing mass spectrometry to achieve parity with sequencing techs, supported by Skyline!
Reposted by Michael MacCoss
October 6, 2025 at 7:38 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
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
Reposted by Michael MacCoss
Staff scientist position in the Mass Spec Lab at the LSU Health New Orleans Neuroscience Center of Excellence lsuhsc.peopleadmin.com/postings/20349
STAFF SCIENTIST OR STAFF SCIENTIST SENIOR
We are seeking a highly motivated PhD Chemist to join our laboratory as a Staff Scientist or Staff Scientist Senior and work on lipidomic and LC- MS/MS. Those with experience or willing to be trained ...
lsuhsc.peopleadmin.com
September 9, 2025 at 11:19 PM
Staff scientist position in the Mass Spec Lab at the LSU Health New Orleans Neuroscience Center of Excellence lsuhsc.peopleadmin.com/postings/20349
Reposted by Michael MacCoss
(J Proteom Res) [ASAP] Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide: Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00297 #MassSpecRSS
[ASAP] Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide
Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00297
dlvr.it
August 14, 2025 at 11:04 AM
(J Proteom Res) [ASAP] Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide: Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00297 #MassSpecRSS
Reposted by Michael MacCoss
🚨 Webinar Alert! 🚨
Carafe enables high-quality in silico spectral library generation for data independent acquisition proteomics
📅 August 5 - 19:00 Seattle / August 6 - 10:00 Beijing
💡 Don't miss this chance to learn from the experts
#Proteomics
Carafe enables high-quality in silico spectral library generation for data independent acquisition proteomics
📅 August 5 - 19:00 Seattle / August 6 - 10:00 Beijing
💡 Don't miss this chance to learn from the experts
#Proteomics
August 1, 2025 at 10:21 AM
🚨 Webinar Alert! 🚨
Carafe enables high-quality in silico spectral library generation for data independent acquisition proteomics
📅 August 5 - 19:00 Seattle / August 6 - 10:00 Beijing
💡 Don't miss this chance to learn from the experts
#Proteomics
Carafe enables high-quality in silico spectral library generation for data independent acquisition proteomics
📅 August 5 - 19:00 Seattle / August 6 - 10:00 Beijing
💡 Don't miss this chance to learn from the experts
#Proteomics
Reposted by Michael MacCoss
Our CNHUPO OES webinar 7 will be from Bo Wen at MacCoss Lab & Noble Lab at University of Washington, hosted by Wenfeng Zeng at Westlake University (10AM on Aug 6 UTC+8). Mark your calendar to learn more about DIA proteomics! @maccoss.bsky.social @us-hupo.org
August 1, 2025 at 5:23 AM
Our CNHUPO OES webinar 7 will be from Bo Wen at MacCoss Lab & Noble Lab at University of Washington, hosted by Wenfeng Zeng at Westlake University (10AM on Aug 6 UTC+8). Mark your calendar to learn more about DIA proteomics! @maccoss.bsky.social @us-hupo.org
Reposted by Michael MacCoss
Improvements to Casanovo, a deep learning de novo peptide sequencer www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
July 29, 2025 at 6:20 PM
Improvements to Casanovo, a deep learning de novo peptide sequencer www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
Reposted by Michael MacCoss
Success! We've now run almost 2000 mouse cortex and plasma samples through this assay so expect more publications referencing it very soon. Much thanks to the Skyline team and @maccoss.bsky.social #modelad #teammassspec #proteomics www.tandfonline.com/doi/full/10....
Analytical development and application of a targeted liquid chromatography-tandem mass spectrometry assay for chimeric aducanumab
A sensitive and specific liquid chromatography-tandem mass spectrometry assay was developed for the quantification of chimeric aducanumab (chAdu), a therapeutic antibody targeting pathological amyl...
www.tandfonline.com
July 25, 2025 at 7:16 PM
Success! We've now run almost 2000 mouse cortex and plasma samples through this assay so expect more publications referencing it very soon. Much thanks to the Skyline team and @maccoss.bsky.social #modelad #teammassspec #proteomics www.tandfonline.com/doi/full/10....
Reposted by Michael MacCoss
My latest academic work on applied NLP is now published in Analytical Chemistry:
"A Large Language Model–Powered Map of Metabolomics Research"
Paper: pubs.acs.org/doi/10.1021...
App: metascape.streamlit.app/
"A Large Language Model–Powered Map of Metabolomics Research"
Paper: pubs.acs.org/doi/10.1021...
App: metascape.streamlit.app/
July 3, 2025 at 9:49 PM
My latest academic work on applied NLP is now published in Analytical Chemistry:
"A Large Language Model–Powered Map of Metabolomics Research"
Paper: pubs.acs.org/doi/10.1021...
App: metascape.streamlit.app/
"A Large Language Model–Powered Map of Metabolomics Research"
Paper: pubs.acs.org/doi/10.1021...
App: metascape.streamlit.app/
Reposted by Michael MacCoss
De novo DIA searching and a Nextflow workflow to run it and generate Skyline documents? Yes!
www.nature.com/articles/s41...
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
July 1, 2025 at 11:13 PM
De novo DIA searching and a Nextflow workflow to run it and generate Skyline documents? Yes!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
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
July 2, 2025 at 5:19 PM
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...
www.nature.com/articles/s41...
The Mag-Net paper is out! We've now put 1000s of plasma samples through this protocol and we know others have too. We've used it to study dozens of diseases. Looking forward to seeing what others apply this towards. The preprint already has >39 citations. www.nature.com/articles/s41...
Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome - Nature Communications
Authors report MagNet, a plasma extracellular vesicle (EV) enrichment strategy using magnetic beads. Proteomic interrogation of this plasma EV fraction enables the detection of proteins that are beyon...
www.nature.com
July 1, 2025 at 2:01 PM
The Mag-Net paper is out! We've now put 1000s of plasma samples through this protocol and we know others have too. We've used it to study dozens of diseases. Looking forward to seeing what others apply this towards. The preprint already has >39 citations. www.nature.com/articles/s41...
Reposted by Michael MacCoss
Proteomics Market Size Worth USD 90.83 Billion by 2034 | CAGR: 12.7%
The global proteomics market is witnessing remarkable growth as breakthroughs in life sciences and biomedical research continue to accelerate. The market, valued at USD 27.54 billion in 2024, is expected to rise to USD 30.97…
The global proteomics market is witnessing remarkable growth as breakthroughs in life sciences and biomedical research continue to accelerate. The market, valued at USD 27.54 billion in 2024, is expected to rise to USD 30.97…
Proteomics Market Size Worth USD 90.83 Billion by 2034 | CAGR: 12.7%
The global proteomics market is witnessing remarkable growth as breakthroughs in life sciences and biomedical research continue to accelerate. The market, valued at USD 27.54 billion in 2024, is expected to rise to USD 30.97 billion in 2025, and is projected to reach USD 90.83 billion by 2034, exhibiting a healthy compound annual growth rate (CAGR) of 12.7% over the forecast period from 2025 to 2034. Market Overview Proteomics, the large-scale study of proteins, is playing a vital role in transforming biomedical research, clinical diagnostics, and drug development. Proteins serve as essential biomarkers for disease detection, prognosis, and therapeutic targeting, making proteomics indispensable for advancing precision medicine.
beeswire.com
June 29, 2025 at 12:45 PM
Proteomics Market Size Worth USD 90.83 Billion by 2034 | CAGR: 12.7%
The global proteomics market is witnessing remarkable growth as breakthroughs in life sciences and biomedical research continue to accelerate. The market, valued at USD 27.54 billion in 2024, is expected to rise to USD 30.97…
The global proteomics market is witnessing remarkable growth as breakthroughs in life sciences and biomedical research continue to accelerate. The market, valued at USD 27.54 billion in 2024, is expected to rise to USD 30.97…
Reposted by Michael MacCoss
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!
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!
June 26, 2025 at 3:30 PM
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!
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!
Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.
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...
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
June 16, 2025 at 6:52 PM
Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.
Reposted by Michael MacCoss
RIP Alan Marshall, one of the greatest mass spectrometrists ever, and a great human to boot.
nationalmaglab.org/careers/meet...
nationalmaglab.org/careers/meet...
Alan Marshall: A scientist and a Gentleman - MagLab
Meet one of the greatest innovators in the history of mass spectrometry, hard at work.
nationalmaglab.org
June 12, 2025 at 2:03 PM
RIP Alan Marshall, one of the greatest mass spectrometrists ever, and a great human to boot.
nationalmaglab.org/careers/meet...
nationalmaglab.org/careers/meet...
Reposted by Michael MacCoss
My Canadian university, Queen's, is offering TWENTY 4-year funded PhDs (40k CAD/yr) for a student of ANY citizenship who has been accepted at a top 100 US university but have had offer rescinded OR are reconsidering offer due to US policy.
Details found here👇
www.queensu.ca/grad-postdoc...
Details found here👇
www.queensu.ca/grad-postdoc...
Queen’s Special U.S. Doctoral Recruitment Initiative | School of Graduate Studies and Postdoctoral AffairsDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown...
Queen’s University is a globally engaged, research-intensive institution dedicated to attracting and supporting exceptional PhD students who will significantly advance our research mission.
www.queensu.ca
June 5, 2025 at 3:31 PM
My Canadian university, Queen's, is offering TWENTY 4-year funded PhDs (40k CAD/yr) for a student of ANY citizenship who has been accepted at a top 100 US university but have had offer rescinded OR are reconsidering offer due to US policy.
Details found here👇
www.queensu.ca/grad-postdoc...
Details found here👇
www.queensu.ca/grad-postdoc...