Dan Polasky

48 posts

Dan Polasky

Dan Polasky

@DanPolasky

Research Investigator @ nesvilab - University of Michigan | mass spectrometry, data analysis and software, ion mobility, proteomics

Katılım Haziran 2019
100 Takip Edilen231 Takipçiler
Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
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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Dan Polasky
Dan Polasky@DanPolasky·
@neely615 You can use wine to get everything working I think, but not something I've done personally
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Dan Polasky
Dan Polasky@DanPolasky·
@neely615 @lgamon Yeah we don't officially support Mac OS but FragPipe itself and tools that are in Java should work
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Luke Gamon
Luke Gamon@lgamon·
Anyone ever tried doing database searching on one of the new M1/M2/M3 macs? Either natively or with VMware Fusion to run Windows etc? We've got hardcore PC workstations for large datasets but would be nice to do some quick and dirty searches locally #TeamMassSpec #proteomics
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Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
#FragPipe 21 release, powered by MSFragger 4. New DDA+ mode (chimeric/full isolation window search). Detailed mass offset mode for advanced PTM/chemoproteomics searches. Astral tuning. PTM site localization in DIA reports. Improved support for MSStats FragPipe-Analyst, and more!
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Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
Are you a #FragPipe user attending #HUPO2023 and have a question? Or just want to learn what’s new in MSFragger and other tools (DIA mode, Labile PTMs, MSBooster rescoring, wide window DDA etc). Talk to me, @fcyucn or @DanPolasky if you see us and come to our poster presentations
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Dan Polasky retweetledi
Georges BEDRAN
Georges BEDRAN@GeorgesBEDRAN3·
Excited to share our recent work on the glycosylated immunopeptidome: nature.com/articles/s4146… Huge thanks to all the talented team members! @DanPolasky @AlfaroJav @nesvilab #Cancer #Immunotherapy #CancerResearch
Alexey Nesvizhskii@nesvilab

Unraveling the glycosylated immunopeptidome! Here we describe our HLA-Glyco workflow in #FragPipe, a web resource based on eight large mass spec based immunopeptidome datasets (over 3,400 HLA class II N-glycopeptides), and several interesting observations. nature.com/articles/s4146…

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Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
Unraveling the glycosylated immunopeptidome! Here we describe our HLA-Glyco workflow in #FragPipe, a web resource based on eight large mass spec based immunopeptidome datasets (over 3,400 HLA class II N-glycopeptides), and several interesting observations. nature.com/articles/s4146…
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Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
#MSFragger-Labile manuscript led by @DanPolasky is now out in MCP. Many PTMs (phospho, ADP-rybo, etc.) fragment during MS/MS. By incorporating modification fragmentation into search, we can identify many more modified peptides than conventional searches. mcponline.org/article/S1535-…
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Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
@DanPolasky is heading to Gordon Research Conference on Glycobiology to present "The MSFragger-Glyco Software Suite in FragPipe: A Growing Toolkit for Glycoproteomics Analysis". Ultrafast search, glyco FDR control, MS/MS visualization, LFQ/TMT quantification, and more! #glycotime
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Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
Check out our new review "Recent advances in computational algorithms and software for large-scale glycoproteomics" led by @DanPolasky. We discuss various strategies, new algorithms, and outstanding challenges, including validation of glycan assignments. sciencedirect.com/science/articl…
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Dan Polasky
Dan Polasky@DanPolasky·
@csdawsonn @nesvilab Definitely feasible! We often search 100s of mass offsets for glyco searches using these same labile methods under the hood
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Charlotte Dawson
Charlotte Dawson@csdawsonn·
@nesvilab @DanPolasky Very nice! Is it feasible to search for all 4 bases at once in standard UV crosslinking data (ie not PAR-CLIP)? Or would this expand the search space too much and take forever?
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Dan Polasky retweetledi
Nick Riley
Nick Riley@riley_nm1·
I am getting an opportunity of a lifetime: I will start as an assistant professor at @UWChemistry in the second half of 2023. The @riley_research group will explore questions about extracellular biology using mass spec, glycoproteomics, and chemical biology.
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Dan Polasky retweetledi
Alexey Nesvizhskii
Alexey Nesvizhskii@nesvilab·
What a great collaboration with the @YMerbl lab and others, out today in Nature Biotechnology. #MSFragger and #Philosopher are at the core of a computational workflow for PTM mining of immunopeptidome data. We will also be releasing more HLA-PTM workflows in #FragPipe 19 soon.
Aaron Javitt@AaronJavitt

Over half of the peptides in the #immunopeptidome are still unidentified! Check out our new paper in @NatureBiotech where we develop PROMISE to identify modified HLA peptides and illuminate🔦 MS dark matter, revealing new classes of cancer antigens. nature.com/articles/s4158…🧵1/7

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Keşfet

@Smith_Chem_Wisc @michaellazear @wfondrie @briansearle @DorferV @lgamon @fcyucn @GeorgesBEDRAN3