FragPipe
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Nesvilab
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
I found an issue (or rediscovered?) I have a custom database with a sequence of high abundant, spike in protein. If I add the sequence as >alphaamylase it is identified...
Dear FragPipe team, As a new user, I ran into an issue when attempting to run 'open search' using the latest version of Fragpipe. The error occurs during PSM validation...
I encountered some unusual problems， when I use fragpipe to analysis a batch of .raw files, the same parameters on different computers sometimes return error as "This application has requested...
Hello, I have been using the isobaric quant tool in FragPipe 17 and now version 18, and I wanted to report an unexpected result when using different "ratio to abundance"...
The Peptides which are reported in the ion_label_quant.tsv, in the modified sequence, are mapped directly to fasta file based on sequence matching, but often that peptide couldn't have arisen from...
I'm interested in extracting the list of matched b/y ions (not just total number of matched ions) for each PSM identified by MSFragger. Could you kindly instruct me on how...
This is a bug reported by emails. I put it here in case we forget it. It also let potential affected users know: human contaminant proteins are always not marked...
I'm using philosopher.yml for TMT quantification. I noticed that even though I don't apply any normalisation or correction the TMT abundances on peptide level differ from the abundances on protein...
Hi, i would like to use MSFragger to generate a library from DDA PASEF data for a subsequent diaPASEF search with DIA-NN. Overall, this works. However, when looking at the...
