Research Investigator @ nesvilab - University of Michigan | mass spectrometry, data analysis and software, ion mobility, proteomics
Joined June 2019
- Tweets48
- Following99
- Followers229
- Likes77
Dan Polasky retweeted
Led by @DanPolasky and in collaboration with @Smith_Chem_Wisc 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…
Dan Polasky retweeted
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
Dan Polasky retweeted
#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!
Dan Polasky retweeted
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
Dan Polasky retweeted
@GeorgesBEDRAN3, @DanPolasky from
@nesvilab and colleagues present a computational workflow for identifying glycosylated peptides from mass spectrometry-based immunopeptidome data and investigate the properties of glycosylated MHC associated peptides
nature.com/articles/s41467-0…
Dan Polasky retweeted
Excited to share our recent work on the glycosylated immunopeptidome: nature.com/articles/s41467-0…
Huge thanks to all the talented team members!
@DanPolasky @AlfaroJav @nesvilab
#Cancer #Immunotherapy #CancerResearch
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/s41467-0…
Dan Polasky retweeted
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/s41467-0…
Dan Polasky retweeted
#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-…
Dan Polasky retweeted
@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
Dan Polasky retweeted
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/ar…
Dan Polasky retweeted
We (led by @DanPolasky) describe a new, flexible Labile Mode of #MSFragger in #FragPipe that can tailor labile PTM searches to their specific fragmentation characteristics. Improved ID rates for phospho, RNA-crosslinked, ADP-ribosylated peptides and more. biorxiv.org/content/10.1101/…
Dan Polasky retweeted
I think I've said most of what I want to say here, so I'll just post it and let others take the mic
pubs.acs.org/doi/full/10.102…
Dan Polasky retweeted
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.
Dan Polasky retweeted
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.
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/s41587-0…🧵1/7
Dan Polasky retweeted
Nice to see our review on glycoproteomics out today in @MethodsPrimers, it was alot fun putting this together with @StacyMalaker @BagdonaiteIeva @DanPolasky @riley_nm1 and many more #glycotime – at Melbourne, Victoria
Our latest Primer summarizes glycoproteomic techniques and best practices for their use @kattesch @StacyMalaker @BagdonaiteIeva
go.nature.com/3xQ84td
Dan Polasky retweeted
#ASMS2022 come learn about glycoproteomics workflows in #FragPipe and chat with @DanPolasky at his poster ThP187 about MSFragger-Glyco, new glycan assignment with FDR scoring (see recent paper in case you missed mcponline.org/article/S1535-…), quantification, MS/MS spectral viewer, etc
Dan Polasky retweeted
Whoa! I'm really liking @nesvilab Fragpipe 18's new built in spectra viewer! If you have ddaPASEF data it's a great free way to view the PSM's
Dan Polasky retweeted
Love #FragPipe, or only heard about it? If at #ASMS2022, come today (Monday) to our poster 257. Tell us why you like it, what can be improved, or perhaps propose a new collaboration. I will come earlier and will stay as long as people are coming, @fcyucn and @DanPolasky also here
We are pleased to announce the 2022 @myABRF PRG Multi-laboratory Glycoproteomics Eggs-ercise. Building off our success with accessible materials (aka beer), and goal of education, we are excited to engage the global community.
zenodo.org/record/6475999#.Y…
If you are interested, please sign up with this link (pass it around!). We are still working out the specifics, but expect to send out instructions this summer, get data back this fall/winter, and report results next spring.
tinyurl.com/proteomelette
Note: we couldn't just do the beer study twice, but at least we still have beer.
xitter.gq/neely615/status/152695…
If you want to find out more about the PRG in general, check out the website.
abrf.org/proteomics-prg-
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