Michael Riffle
@mriffle.bsky.social
I love doing science, writing software, solving new problems, and making things. My day job: proteomics, bioinformatics, data science, and lots of writing and figure making. Also very into travelling & photography.
Reposted by Michael Riffle
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
September 6, 2025 at 11:09 PM
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
Reposted by Michael Riffle
Do you or your lab use the Skyline software for #MassSpectrometry #proteomics? I'm looking for instructors to help with this year's Skyline Online, a virtual workshop/crash-course for all things Skyline! I'm especially looking for early career researchers for this opportunity. Please DM!
September 6, 2025 at 5:11 PM
Do you or your lab use the Skyline software for #MassSpectrometry #proteomics? I'm looking for instructors to help with this year's Skyline Online, a virtual workshop/crash-course for all things Skyline! I'm especially looking for early career researchers for this opportunity. Please DM!
OK. I must go here.
August 31, 2025 at 10:55 PM
OK. I must go here.
Reposted by Michael Riffle
Cascadia from @wnoble.bsky.social is a mass spec-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a range of instruments and experimental protocols. www.nature.com/articles/s41...
July 7, 2025 at 10:31 PM
Cascadia from @wnoble.bsky.social is a mass spec-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a range of instruments and experimental protocols. www.nature.com/articles/s41...
Interesting opportunity!
Genome Sciences is looking for a Director of Departmental Computing. This is a rare opportunity for someone interested in leading our excellent IT team, building and maintaining computational infrastructure, and working closely with our faculty and labs uwhires.admin.washington.edu/ENG/candidat...
UW Human Resources
University of Washington Human Resources
uwhires.admin.washington.edu
July 12, 2025 at 5:46 PM
Interesting opportunity!
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...
Reposted by Michael Riffle
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 Riffle
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....
pubs.acs.org/doi/full/10....
June 17, 2025 at 8:57 PM
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....
pubs.acs.org/doi/full/10....
Reposted by Michael Riffle
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reply to: Reply to: False positives in the study of memory-related gene expression
In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…
liorpachter.wordpress.com
June 16, 2025 at 9:31 PM
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reposted by Michael Riffle
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 Riffle
Let's start with - there is no data availability statement anywhere. There is no source data. I see no evidence whatsoever to support that any experiments detailed in this study were performed at all. Unless I'm missing something huge - Shame on @jacs.acspublications.org and these reviewers.
June 13, 2025 at 1:17 PM
Let's start with - there is no data availability statement anywhere. There is no source data. I see no evidence whatsoever to support that any experiments detailed in this study were performed at all. Unless I'm missing something huge - Shame on @jacs.acspublications.org and these reviewers.
Incredible shot of one of my favorite places in the world.
Lake Crescent for lady aurora tonight! Or last night? Idk, it's 4 AM and I'm still buzzing from taking such pretty photos tonight.
#lakecrescent #aurora #arouraborealis #northernlights #purple #lightshow #PNW #pnwlife #womeninphotography #yourshotphotographer #shotonsony
#lakecrescent #aurora #arouraborealis #northernlights #purple #lightshow #PNW #pnwlife #womeninphotography #yourshotphotographer #shotonsony
June 3, 2025 at 11:56 AM
Incredible shot of one of my favorite places in the world.
Reposted by Michael Riffle
New Preprint ... This was a bit different of a project than what we normally do for hardware comparisons. I think there is a lot of potential in the methods mentioned here for calibrating the instrument response to a common scale. Nice work by @chrhsu.bsky.social!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Evaluation of an Orbitrap Astral Zoom mass spectrometer prototype 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...
www.biorxiv.org
June 1, 2025 at 4:47 AM
New Preprint ... This was a bit different of a project than what we normally do for hardware comparisons. I think there is a lot of potential in the methods mentioned here for calibrating the instrument response to a common scale. Nice work by @chrhsu.bsky.social!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Michael Riffle
Interested in prediction tasks involving peptide mass spectra? Our foundation model uses pre-trained spectrum representations learned by a de novo sequencing model to solve many tasks better and with less data, from recognizing chimeras to separating N- and O-glycopeptides. arxiv.org/abs/2505.10848
Foundation model for mass spectrometry proteomics
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrument...
arxiv.org
May 22, 2025 at 11:49 AM
Interested in prediction tasks involving peptide mass spectra? Our foundation model uses pre-trained spectrum representations learned by a de novo sequencing model to solve many tasks better and with less data, from recognizing chimeras to separating N- and O-glycopeptides. arxiv.org/abs/2505.10848
Reposted by Michael Riffle
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.
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.
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.
May 15, 2025 at 1:24 AM
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.
Reposted by Michael Riffle
Attending #ASMS2025 in Baltimore? Interested in quantitative proteomics? Join us Sunday Afternoon, June 1st for our annual Skyline User Group Meeting. We have a fantastic group of speakers. For information and to Register:
skyline.ms/project/home...
#massspectrometry #proteomics #metabolomics
skyline.ms/project/home...
#massspectrometry #proteomics #metabolomics
Start Page: /home/software/Skyline/events/2025 User Group Meeting at ASMS
skyline.ms
May 5, 2025 at 6:41 AM
Attending #ASMS2025 in Baltimore? Interested in quantitative proteomics? Join us Sunday Afternoon, June 1st for our annual Skyline User Group Meeting. We have a fantastic group of speakers. For information and to Register:
skyline.ms/project/home...
#massspectrometry #proteomics #metabolomics
skyline.ms/project/home...
#massspectrometry #proteomics #metabolomics
"Harmful algal blooms (HABs) have become a worldwide environmental and human health problem, stressing the urgent need for a reliable forecasting tool. "
Excited to have been a part of this work out of the Nunn lab (www.environmentalproteomics.org) to find peptide biomarkers for predicting HABs.
Excited to have been a part of this work out of the Nunn lab (www.environmentalproteomics.org) to find peptide biomarkers for predicting HABs.
Harmful algal blooms are preceded by a predictable and quantifiable shift in the oceanic microbiome - Nature Communications
Harmful algal blooms (HABs) pose negative worldwide impacts that could be minimized through the development of a forecasting tool. Quantitative analysis of peptides produced by a coastal microbiome pr...
www.nature.com
April 29, 2025 at 9:35 PM
"Harmful algal blooms (HABs) have become a worldwide environmental and human health problem, stressing the urgent need for a reliable forecasting tool. "
Excited to have been a part of this work out of the Nunn lab (www.environmentalproteomics.org) to find peptide biomarkers for predicting HABs.
Excited to have been a part of this work out of the Nunn lab (www.environmentalproteomics.org) to find peptide biomarkers for predicting HABs.
Is it just me, or are LLMs getting snarkier? I'm definitely noticing some attitude.
April 29, 2025 at 9:13 PM
Is it just me, or are LLMs getting snarkier? I'm definitely noticing some attitude.
Reposted by Michael Riffle
#Skyline #proteomics #MassSpec
@maccoss.bsky.social Hope everyone that uses Skyline shows their support skyline.ms/project/home...
@maccoss.bsky.social Hope everyone that uses Skyline shows their support skyline.ms/project/home...
April 21, 2025 at 10:10 PM
#Skyline #proteomics #MassSpec
@maccoss.bsky.social Hope everyone that uses Skyline shows their support skyline.ms/project/home...
@maccoss.bsky.social Hope everyone that uses Skyline shows their support skyline.ms/project/home...
Reposted by Michael Riffle
Check out our upcoming webinar! In this US HUPO X ABRF crossover event, you'll learn about where AI is currently used in proteomics and where it may be transformative in the future. Register now: ow.ly/tKB750VB1PN 🧪
April 16, 2025 at 6:00 PM
Check out our upcoming webinar! In this US HUPO X ABRF crossover event, you'll learn about where AI is currently used in proteomics and where it may be transformative in the future. Register now: ow.ly/tKB750VB1PN 🧪
Reposted by Michael Riffle
Skyline-daily 24.1.1.449 was just released with support for importing DIA-NN v2 results, integrated Comet searching, many performance improvements and bug fixes. Lots of new things in the works.
skyline.ms/skyline.url
#proteomics #massspec #proteomicsky
skyline.ms/skyline.url
#proteomics #massspec #proteomicsky
skyline.ms
March 26, 2025 at 4:55 AM
Skyline-daily 24.1.1.449 was just released with support for importing DIA-NN v2 results, integrated Comet searching, many performance improvements and bug fixes. Lots of new things in the works.
skyline.ms/skyline.url
#proteomics #massspec #proteomicsky
skyline.ms/skyline.url
#proteomics #massspec #proteomicsky
Reposted by Michael Riffle
Are you going to #ASMS2025 and interested in learning about #AI and #MachineLearning for #MassSpec? 🤖
Sign up for our short course, "05 Machine Learning for Mass Spectrometry Data Analysis" while there is still space! www.asms.org/conferences/...
🧵 1/3
Sign up for our short course, "05 Machine Learning for Mass Spectrometry Data Analysis" while there is still space! www.asms.org/conferences/...
🧵 1/3
Short Courses
www.asms.org
March 26, 2025 at 4:07 PM
Are you going to #ASMS2025 and interested in learning about #AI and #MachineLearning for #MassSpec? 🤖
Sign up for our short course, "05 Machine Learning for Mass Spectrometry Data Analysis" while there is still space! www.asms.org/conferences/...
🧵 1/3
Sign up for our short course, "05 Machine Learning for Mass Spectrometry Data Analysis" while there is still space! www.asms.org/conferences/...
🧵 1/3
Reposted by Michael Riffle
If you want a free way to organize, filter, share, QC, and visualize proteomics DDA search results you should check out Limelight. A fantastic tool spearheaded by @mriffle.bsky.social
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines
Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein–protein interac...
pubs.acs.org
March 12, 2025 at 12:59 AM
If you want a free way to organize, filter, share, QC, and visualize proteomics DDA search results you should check out Limelight. A fantastic tool spearheaded by @mriffle.bsky.social
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Aaaaaaand, I'm done w Chrome.
December 20, 2024 at 12:31 AM
Aaaaaaand, I'm done w Chrome.