Searching your diaPASEF data for unknown modifications (Open) non-common PTMs or semitryptic peptides directly w/o need for spectral libraries? Here you go! biorxiv.org/content/10.110…

Meet our #FragPipe team at #ASMS2024! We present on DDA+ , DIA, and diaPASEF methods, metaproteomics, benchmarking deep learning prediction tools, DIA glycoproteomics, TPP workflow, Skyline integration with FragPipe, and more! As usual you can probably find me near our posters!

Looking forward to ASMS 2024 and especially the new chemoproteomics sessions this year! Come to Alex Campos and my workshop to learn more about the frontiers of chemoproteomics-- Monday 5:45-7PM ROOM 208AB (Level 2)

Thank you so much for helping presenting my poster, Alexey! Friends, if you saw me, but I smiled and walked away, it wasn’t because I didn’t want to have a chat with you. I really wanted to but I can’t make a “controllable sound” due to unknown reasons 😭

To get there was quite a journey, but finally it is out: Our massive High-Throughput #Proteomics study on sepsis with >4500 LCMS runs using #Evosep, #Bruker #TimsTOF and #Fragpipe: science.org/doi/10.1126/sc…

So happy to see this paper out. It was a collaboration that made us work really hard to make IonQuant and LFQ workflow in #FragPipe faster, more memory efficient, capable of processing thousands of timsTOF files. Our new computational work is often driven by challenges like this

Very interesting bioRxiv by the group of Alexey Nesvizhskii and Fengchao Yu. They developed the tool diaTracer for fully integrated, library-free analysis of diaPASEF data from a Bruker timsTOF in FragPipe. Looking forward to exploring this on our data. biorxiv.org/content/10.110…

Thrilled to share our groups' new SEE-CITE photoaffinity labeling methodology where we installed a silyl cleavable linker between the diazirine and MOI to enable head-to-head interactomics. Spearheaded by Sho Takechi and Chau Ngo and now up on ChemRxiv chemrxiv.org/engage/chemrxi…

A key piece of this study was the new PAL localization mode that is built into the new #FragPipe V22 release thanks to Fengchao Yu and Alexey Nesvizhskii

Fengchao Yu Alexey Nesvizhskii FragPipe now reports the hyperscores for each amino acid in a peptide sequence based on both shifted (PAL modified) and unshifted ions, which allows the label to be localized to either a single amino acid or within a region of the peptide sequence, depending on sequence coverage

Our Proteomics summer school is back for 2024! Don't want to miss it this year as we have some cool group research planned! The link below works even though it says 2023 :) proteomics.ucdavis.edu/events/2023-ha…

Led by Dan Polasky and in collaboration with MetaMorpheus @metamorpheus.bsky.social lab, we improved #FragPipe for O-glycoproteomics analysis. It provides fast (#MSFragger-Glyco), proteome-wide, quantitative results (LFQ,TMT), and incorporates O-Pair for glycosite localization! link.springer.com/article/10.100…

I am enjoying my visit to Madison to give a lecture and a short #FragPipe tutorial at the North American MS Summer School ncqbcs.com/resources/trai…. At the some time, Fengchao Fengchao Yu is flying to San Francisco to do the same at the UCSF proteomics course. wiitalab.ucsf.edu/events/biologi….

Fun running our 1st hands-on “biological #proteomics for beginners” workshop @ucsf w Dr. Sanjeeva Srivastava. packed house for scientists across the Bay Area. Thanks to Fengchao Yu for coming from Ann Arbor to lead our analysis tutorial in Fragpipe and Rob Moritz for keynote lecture!

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.

Skyline version 24.1 is out. What the Skyline team is doing is amazing, they are a role model for all academic bioinformatics labs. We are fortunate to work with them on #FragPipe-Skyline integration skyline.ms/project/home/s…

This is how I started my Friday 🤷🏻‍♂️ (There are more computers turned into blue screen but Twitter only lets me upload four pics)

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…

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