#fragpipe — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #fragpipe, aggregated by home.social.
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Why is FragPipe/MSFragger always bailing out with a memory succession problem on the last slice of the main search - always at the very end.. unbelievable #fragpipe
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Anyone thought about forcing something like a flexible modification group in FragPipe - e.g., to have either dimethylation or acetylation on N-termini without constraints of having all as variable modifications for semi-specific searches? I am almost tempted to try dimethylation as fixed modification (e.g., + 28 Da)with variable mod for putative acetylations (+ 14 Da). #Proteomics #FragPipe
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RT @: 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
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RT @: 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
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Want to thank everyone here for some stellar discussion on SAAVs and searching.
Follow up: is there a SAAV-only open search option? So open-search but constrain fitting delta mass unknowns to AAs only (no funky ptms). I am off to poke around in #FragPipe but figured the crowd might know better.
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Want to thank everyone here for some stellar discussion on SAAVs and searching.
Follow up: is there a SAAV-only open search option? So open-search but constrain fitting delta mass unknowns to AAs only (no funky ptms). I am off to poke around in #FragPipe but figured the crowd might know better.
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RT @kalonji_08: Does anyone know how to Install #Fragpipe and all dependencies in Linux ? I’m having some #Java problem and I wouldn’t want to risk running it on my laptop. Please assist Thanks #massspec #Bioinformatics #proteomics
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RT @kalonji_08: Does anyone know how to Install #Fragpipe and all dependencies in Linux ? I’m having some #Java problem and I wouldn’t want to risk running it on my laptop. Please assist Thanks #massspec #Bioinformatics #proteomics
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A question for all the DiaNN experts here: I run DiaNN through FragPipe 19.1 and tried to see if there is a big deal in the "Unrelated runs" option in FragPipe for DiaNN. I totally understand the ID data differing, but not why the Total.Quantity if different for both run modi, though the MS1 and MS2 Quantities are identical?!? (in red the difference) #FragPipe #DiaNN
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#TeamMassSpec
I use #FragPipe developed by the Nesvizhskii lab for #proteomics data analysis. The latest update has a link to analyze the results using a version of #LFQAnlyst compatible with FragPipe output called #FragPipe-Analyst.
http://fragpipe-analyst.nesvilab.org/
This is a powerful R statistical analysis workflow that anybody can quickly use to get descriptive and differential abundance results directly from the FragPipe output. Thanks @nesvilab -
#TeamMassSpec
I use #FragPipe developed by the Nesvizhskii lab for #proteomics data analysis. The latest update has a link to analyze the results using a version of #LFQAnlyst compatible with FragPipe output called #FragPipe-Analyst.
http://fragpipe-analyst.nesvilab.org/
This is a powerful R statistical analysis workflow that anybody can quickly use to get descriptive and differential abundance results directly from the FragPipe output. Thanks @nesvilab