Lab News & Updates

Excited to see this latest paper published in JPR. For years we’ve wanted a simple way to standardize the signal between mass spectrometry instrumentation. Here we use the precision of an intra spectrum ratio to assess the relationship between the reported signal and the number of ions. We use this strategy to assess the improvement in the Orbitrap Astral Zoom over the original and to evaluate the effect of different acquisition strategies. Looking forward to seeing others apply this approach in the evaluation of other instruments. Great work by graduate student Chris Hsu.

The Skyline Team and our invited instructors are pleased to announce the return of the wildly popular Skyline Online course coming this October 2025. These sessions have always filled up quickly. Do not put off registering if you want to attend.

Skyline Online will offer two 2-day sessions on Proteomics (3, 4) topics and a 3-day session on Small Molecule (1-and-2) topics:

-Session 1 and 2 - Intro and Advanced Small Molecule Topics - BONUS! 3 Days, same price - Oct 8-10 -Session 3 - Introduction to Skyline for Proteomics - Oct 14-15 -Session 4 - Advanced Proteomics Topics - Oct 17-18

Register Now

Weeklong Skyline Course in Seattle! Great speakers and participation in our yearly course.

New Publication in Nature Methods. A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data. Great collaborative project pushed by Justin Sanders in the Noble Lab. 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 proven wrong.

The Mag-Net paper is out in Nature Communications. Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome. This started as a pandemic side project of Chris Wu’s and we now have many variants on the idea. We’ve now put 1000s of plasma samples through this protocol and we know others have too. This has been a game changer for how we view biofluid proteomics.

Skyline User Group Meeting at ASMS. Another year and another fantastic user group meeting. We had 10 fantastic talks from colleagues describing how they are using Skyline in their research. See recordings on the Skyline website.