Low input-proteomics on a versatile Q-LIT

If you’re in the mass spectrometry-based proteomics community, there’s a good chance you’re either attending or keeping track of the new releases going on this weekend by various vendors. In the past 6 weeks, Brian Searle and I have worked with some amazing people at Thermo Scientific, including Philip Remes, Cristina Jacob, and Lilian Heil. Along with our collaborators a Thermo, we worked with the talented immunologists at OSU to develop low-input PRM assays from DIA experiments for immune cell subsets. We were able to use a prototype instrument to collect data on the T cell subsets and optimize PRMs for low-input. Searle Lab Paper: https://www.biorxiv.org/content/10.1101/2024.05.31.596891v1

The MacCoss lab at the University of Washington has been using DIA to select targets for SRM/PRM for years. You can read more about it in this recent preprint from Deanna Plubell and the MacCoss Lab: https://www.biorxiv.org/content/10.1101/2024.05.29.596554v1 The main idea within that work is that we can get an idea of what interference will be present for SRMs a DIA chromatogram library.

If you’re interested more in checking out a comparison of a triple quad and the Stellar instrument, I would highly recommend checking out Philip Remes’s new paper here: https://www.biorxiv.org/content/10.1101/2024.05.31.596848v1 Its a great read, and incorporates Philip’s new software PRM conductor, which is SUPER user friendly, has a nice user interface, and is great for making larger scale PRMs (in the range of 1000’s of peptides). The work that we performed was scheduled with EncyclopeDIA, which can allow you to more specifically curate the PRM generation, with the overall goal of targeting in the range of 100’s of peptides.

Published: 06-10-2024