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Rethink the analysis of DDA data! Blurring the boundary between DDA, WWA, and DIA, #MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search. Fully integrated in #FragPipe, simply annotate your DDA files as DDA+ and RUN. biorxiv.org/content/10.110…

Come to my poster at HUPO on Tuesday! Direct spectrum-centric analysis of diaPASEF data using diaTracer and #FragPipe. See how well it works for spatial proteomics, CSF, plasma, HLA, PTMs and more! Updated preprint: biorxiv.org/content/10.110…. With co-authors Kai, Fengchao, Guo Ci.

I had to shorten my trip to Dresden for #HUPO2024 and have a room for Friday and Saturday night, and the following Wednesday night, that will sit empty. They require 14 day cancelation notice. If anyone in a desperate need for a place to stay on those nights, email me.

Nice protocol manuscript on low-input proteomics, with a description of the parameters in the LFQ-MBR workflow of #FragPipe the authors used.

Kevin Yang from the Alexey Nesvizhskii closing the data analytics session by showing the power of MSFragger for scp-MS - incredible what free, academic software can do! #iSCMS2024

Another great collaboration with the Keri Backus' lab, where we implemented a two stage search in #FragPipe to identify gain-of-cys mutations and variants proximal to reference cysteines. Two-stage searches can be useful for many applications, and they ensure group-specific FDR.

If your presentation falls on Halloween, do it in style! Here is Yi (Leo) Hsiao, Bioinformatics Ph.D. student in the lab, presenting his FragPipe-Analyst tool at today's "Tools and Technology" seminar series at the University of Michigan. #FragPipe medschool.umich.edu/events/tools-t…

Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants mdpi.com/3029520. Glad to see #FragPipe/#MSFragger showing the most conservative and effective performance (lowest false discovery match ratio (FDMR))

Very nice paper in Science, showing that N-glycosylation can also function as a degradation signal, similar to Ubiq: science.org/doi/10.1126/sc…. Glad to see the authors used our #FragPipe/#MSFragger-Glyco “Glyco-N-LFQ” workflow for quantitative glycoproteomics data analysis.

Ok, my friends led, I followed. A few clicks, and here we go. Loaded the first photo I found on the disk (note to myself to change it later, way too serious). But 0 followers!! Now I know the feel of social isolation! Help me out there. I will not be leaving X entirely, not yet.

Great to see them apply the proteome-wide profiling method for electrophile reactivity and selectivity that we developed together with Alexey Nesvizhskii in Fragpipe in this exciting system. chemrxiv.org/engage/chemrxi…

Spent a great day in Barcelona at the EMBO Targeted Proteomics course hosted by sabidolab, talking about our DIA tools and helping his team with a hands-on tutorial on FragPipe, FragPipe-Analyst, and Skyline integration, from installation and mzML files to pathway-level results.

Big news in QUANTITATIVE proteomics! Researchers from University of Michigan & Monash University have launched FragPipe-Analyst: a user-friendly, web-based tool to complement the popular FragPipe platform. Upload files, analyze, & visualize data with ease. #Precisionmedicine proteomics.cancer.gov/news_and_annou…

.Kai Alexey Nesvizhskii Fengchao Yu present diaTracer, a spectrum-centric tool for diaPASEF data, enabling direct peptide identification and quantification without spectral libraries. #BiotechNatureComms nature.com/articles/s4146…

Our #diaTracer manuscript is out! 10 years ago we established the concept of library-free, direct DIA analysis with DIA-Umpire. DiaTracer now makes it possible to analyze any diaPASEF data, including PTM, semi-tryptic, nonspecific, and even open searches! nature.com/articles/s4146…

Tim Griffin, Alexey Nesvizhskii and Bing Zhang, will have a panel discussion on 'MS-Based #Immunopeptidomics: Challenges and Opportunities in Immuno-Oncology Research' at the #USHUPO2025 conference on 23rd Feb. ushupoconference.org/agenda#1-17403…

See Kasia Kulej #USHUPO2025 poster on Decoding tumor-specific proteomes with integrative proteogenomics using ProteomeGenerator3 (plus comparison of DIA-NN, Spectronaut and MSFragger)

DDA is still great for many applications, and #MSFragger-DDA+ improves peptide identification rates via full isolation window search. Huge boosts in IDs, including Astral DDA! Fully integrated in #FragPipe, simply annotate your DDA files as DDA+ and RUN. nature.com/articles/s4146…

The Nesvizhskii lab has 9 members attending #ASMS2025! 9 posters, contribution to 4 evening workshops, and one Bioinformatics Hub on #FragPipe. Plus multiple collaborative posters with other groups. See you in Baltimore!

Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome ... biorxiv.org/content/10.110… #biorxiv_sysbio