Have you tried the #MSFragger DDA+ mode in #FragPipe that provides big boost in IDs via full isolation window search of DDA data? While we are still working on the manuscript, I am thrilled to see our users are getting great results, e.g. in this new study biorxiv.org/content/10.110…

Conducted the first overseas proteomics workshop at UCSF, co-organized with Arun Wiita. This ambitious and unique event had every participant prepare samples, run MS, and perform data analysis. MS Data Analysis session by Fengchao Yu, demonstrating FragPipe was great success.

This is a great course that covers targeted proteomics and DIA more broadly, with hands-on data analysis sessions taking students from MS data to processed results. Great location in Barcelona, nice evening social events. I am happy to be invited again as one of the instructors.

So happy to see #MSFragger and #FragPipe used in an increasing number of educational workshops and short courses. Thanks Peter Horvatovich and Dave Tabb! Hope the tutorial went well.

I made a few more tutorial videos on the newest versions of DIA-NN & Fragpipe for those new to the software. Because why pay us when you can do it yourself right? youtube.com/@UCDavisProteo…

Congrats to all co-authors! Our dual-probe PhosID-ABPP paper with EGFR-directed probes is now in ACS Chemical Biology. Finding secondary drug binding sites, validating inhibition of ADP/ATP translocase SLC25A4. Many thanks Elena Pohl Lab and HeckLab! pubs.acs.org/doi/10.1021/ac…

Today in Detroit touring the just re-opened old train station building. Left rotting for 30 years, it was brought back to life by Ford after a massive renovation, and what an amazing place it is. And so is the whole city of Detroit. I love it. Am Soc for Mass Spec - time to come to Detroit!

Are you using mass spec based proteomics to study endogenous proteolytic activity? This work describes an R package TermineR for downstream processing (annotation, visualization, differential analysis etc.) of semi-specific search results from #FragPipe. …iencejournals.onlinelibrary.wiley.com/doi/10.1002/pm…

How is it no one yet twitted how amazing was the HUPO-HIPP immunopeptidomics summer school this week in Montreal? Well organized, great talks and posters, engaged audience. I was fortunate they invited me to talk about our work and do #FragPipe tutorial. hupo.org/Human-Immuno-P….

Excited to share our new ChemRxiv preprint that describes CySP3-96 plate-based cysteine chemoproteomic method. Congrats to Flowreen Shikwana and team and thanks to Gustafson Group @ SDSU for the atropisomers! and #SergiLabSupplies Sergii Pochekailov for the low cost resin! chemrxiv.org/engage/chemrxi…

It is getting hard to keep up with all the cool things the Keriann Backus lab is doing! But if you need good examples of how to use #FragPipe for chemical proteomics, look at their papers. Here they use LFQ-MBR workflow for a new proximity labeling based interactome profiling method

Congrats James W. Checco Keriann Backus and Michael Booth on winning this year's ICBS rising star award in chemical biology. Still time to register to hear them speak about their exciting research! chemical-biology.org/page/ICBS2024

Today was the first lecture of my “Proteomics and Metabolomics” course. When I first taught it back in 2006 there were just 5 students. There were 50 today (the max course capacity) and from multiple Departments. The grad students’ interest in these areas has grown tremendously.

Interesting, FAIMS fractionation improves N-terminal peptide identification. Also, glad to see #FrapPipe used. “Ion Mobility–Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen - Molecular & Cellular Proteomics”. mcponline.org/article/S1535-…

Hurry up! Very last days to register to the Practical Course on Targeted #Proteomics in Barcelona next Nov 17-22 📅 Don't miss it! ✏️Registration at: courses.crg.eu/events/targete…

Our #FragPipe-Analyst manuscript is out! pubs.acs.org/doi/10.1021/ac…. Load FragPipe's TMT/ LFQ/DIA quant tables (peptide or protein quant) and get QC, Limma, PCA, volcano plots, heatmaps, do GO/pathway enrichment analysis, all with just a few clicks! Tutorials:fragpipe-analyst-doc.nesvilab.org

Thank you Lena Barra for invitation to contribute to BJOC by review on diagnostic ions mining for identification of small molecule-protein conjugates: beilstein-journals.org/bjoc/articles/…. The review also includes future opportunities and common limitations of chemical proteomics workflow.

Tim Griffin from The GalaxyP Project presents the iPepGen resource (developed in collaboration with Alexey Nesvizhskii from University of Michigan) for immunooncology research at the #ITCR2024 conference.