Michael Riffle

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...

Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:

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.

Indeed, programs like Cursor and Windsurf change the game.

They also probably used a LLM

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!

Also finding it useful for metaproteomics.

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...

De novo DIA searching and a Nextflow workflow to run it and generate Skyline documents? Yes!

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...

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...

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....

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…

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

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.

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.

Love this spot, too! You’ve been hanging out in my neck of the woods!

Nice shot of these falls. I’ve been here a few times and it’s a tricky spot to make an interesting composition.

We are in the post-thinking phase.

Incredible shot of one of my favorite places in the world.

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...

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...

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...

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

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.

This seems like a rather large assumption about Sciex's point of view.

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

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...

"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.

Is it just me, or are LLMs getting snarkier? I'm definitely noticing some attitude.

#Skyline #proteomics #MassSpec
@maccoss.bsky.social Hope everyone that uses Skyline shows their support skyline.ms/project/home...

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 🧪

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