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Alexey Nesvizhskii
@nesvilab
Godfrey D. Stobbe Professor of Bioinformatics at U of Michigan. Trained as a theoretical physicist, now focusing on proteomics and proteogenomics.
Ann Arbor, MI
nesvilab.org
Joined January 2019
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  • Pinned
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    Alexey Nesvizhskii
    @nesvilab
    May 30, 2024
    Friends, #FragPipe 22 has been released, and it's a big update! diaTracer enables spectrum-centric analysis of diaPASEF data. Skyline integration. Koina server for more deep-learning prediction options. DDA+ mode for ddaPASEF. DIA glycoproteomics and new chemoproteomics workflows
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    Alexey Nesvizhskii
    @nesvilab
    Nov 10, 2024
    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.
    science.org
    Regulated N-glycosylation controls chaperone function and receptor trafficking
    One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekee...
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    Alexey Nesvizhskii
    @nesvilab
    Feb 23, 2021
    Well, it's been 20 years now since (February 2001) I took Ruedi Aebersold's course on Proteomics in the Department of Molecular Biotechnology (UW Seattle), all while still working on my Ph.D. in Physics. Certainly changed things for me. Check out the amazing final exam question!
  • user avatar
    Alexey Nesvizhskii
    @nesvilab
    Apr 20, 2023
    I am truly honored to receive the Godfrey Dorr Stobbe Endowed Professorship in Bioinformatics. It was a beautiful ceremony yesterday, with my family in attendance. I thank my colleagues and the leadership for their support, and looking forward to tacking new scientific challenges
    user avatar
    Michigan Pathology
    @UMichPath
    Apr 20, 2023
    Yesterday, Drs. Ulysses Balis and Alexey Nesvizhskii were honored with their named professorships in Pathology Informatics and Bioinformatics.
    Dr. Parkos (left) and Dr. Balis (right) shake hands during the Professorship Ceremony, yesterday, April 19, 2023.
    Dr. Parkos (right) and Dr. Nesvizhskii (middle) stand with Dr. Nesvizhskii’s family for a photo during the Professorship Ceremony, yesterday, April 19, 2023.
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    Alexey Nesvizhskii
    @nesvilab
    Mar 11, 2021
    Announcing the release of #FragPipe 15. Improvements in all modules, including MSFragger and IonQuant. Support for TMT, SILAC, LFQ-MBR quant, FAIMS, open PTM searches, glycoproteomics, HLA/peptidomics, spectral library building for DIA analysis, and more. fragpipe.nesvilab.org
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    Alexey Nesvizhskii
    @nesvilab
    Sep 5, 2021
    On this day 25 years ago I landed in Seattle on a gloomy day. Did not know anything about the city or, frankly, the country. UW Physics was the only Ph.D. program I applied. Came with two small bags, one full of physics books. Still have them in a box, collecting dust. So it goes
  • user avatar
    Alexey Nesvizhskii
    @nesvilab
    May 31, 2022
    #FragPipe 18 release: new visualization module (view/export MS/MS spectra, special options for glycopetides, protein coverage, sorting, etc.)! New: "headless" option to run command line - great for automation/HPC/cloud. New workflows. Upgrades in all tools fragpipe.nesvilab.org
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    Alexey Nesvizhskii
    @nesvilab
    Jan 26, 2022
    Are you a fan of delicious PTMs? On the day when the Wordle's word was SUGAR came out our manuscript in MCP led by @DanPolasky on FDR control for glycan assignments in glycoproteomics. Fully implemented in #FragPipe as part of MSFragger Glyco workflows!
    Multiattribute Glycan Identification and FDR Control for Glycoproteomics
    From mcponline.org
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    Alexey Nesvizhskii
    @nesvilab
    May 27, 2019
    Two more manuscripts on deep learning for MS/MS spectral prediction out in Nat Methods. Kuster lab: nature.com/articles/s4159… and Cox lab: nature.com/articles/s4159…. That should do it. The focus now should be shifting to practical incorporation of such models into existing workflows.
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    Alexey Nesvizhskii
    @nesvilab
    Jan 17, 2024
    My first foray into AI art. I asked AI to draw a small child sitting in front of a computer connected to a mass spectrometer, using #FragPipe to analyze mass spectrometry data. AI decided that the mass spec must have a lot of pipes. But hey, the child looks happy, so I am happy.
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    Alexey Nesvizhskii
    @nesvilab
    Jul 23, 2021
    And now, ladies and gentlemen, welcome #FragPipe 16, led by MSFragger 3.3, featuring updated Philosopher, IonQuant, TMT-Integrator, PTM-Shepherd and - are you ready? - a new addition to the band, PERCOLATOR! Enjoy this proteomics data analysis awesomeness. fragpipe.nesvilab.org
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    Alexey Nesvizhskii
    @nesvilab
    Jul 12, 2023
    PTM-containing peptides often fragment in unexpected ways, hindering their identification. Here we describe a workflow in #FragPipe to find diagnostic spectral features for any PTM, illustrated using chemoproteomics, RNA-xlinks, glyco and ADP-ribo examples
    Content cover image
    Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides
    From nature.com
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    Alexey Nesvizhskii
    @nesvilab
    Dec 6, 2022
    #FragPipe 19 released! New: O-pair site localization for O-glyco. SAINTexpress for interactome scoring. FP-PDV viewer much faster and can show predicted MS/MS spectra. Improved diagnostic ion mining and labile PTM support. PTMProphet works with timsTOF .d. New workflows and more
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    Alexey Nesvizhskii
    @nesvilab
    Sep 24, 2023
    Everyone who is happily reporting crazy ID numbers on Astrals, please read the @mjmaccoss paper carefully. It is very good. The 10% false (or at least non-quantitative) precursor IDs translates to even higher false protein level FDR. Let’s not go back to the proteomics circa 2001
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