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
The razor assignment might make an alternative protein as the razor protein. Since we don't distinguish `I` and `L` in the protein mapping, some peptides might not exist in their...
I would love to see a summary file that reports the samples analyzed (rows) vs. some overall statistics (columns), like psms, peptides, proteins per sample, PTM modified peptides per sample.
Hi, I don't know if this is by design or not, but I've observed differences between all 3 files, combined_protein.tsv, reprint.int.tsv and reprint.spc.tsv. Although the vast majority is similar, some...
I tried to generate a spectrum library from DIA runs on a Thermo QExactiveHF by DIA Umpire using the workflow from the selection box in the workflow menu. I followed...
Hi Guo Ci @guoci , There are outliers in normalized retention time (out of [-100, 200]). It looks like the range needs to be restricted in the range during the...
Hi Guo Ci @guoci , This is an issue from users. They find that some fragments in the spectral library have zero intensity. Could you please follow up and fix...
A suggestion to add the ability to generate mzIdentML reports through the FragPipe interface. Issue with Philosopher: Unsuccessful in using Philosopher with the pipeline mode to generate mzID files. Error...
Hi, I want to analyze a project which includes 2 fractions, membrane and soluble proteins from the same samples. For this project, LFQ normalization should be performed separately for the...
Hi, we're encountering an error while searching an iTraq4 dataset from CPTAC. Looks like one of the pepXML is corrupted judging on the file sizes. How should we work around...
Hi, I am using the DIA_SpecLib pipeline on Fragpipe to generate a library from 150 DDA files. Previously, using 10 files from the DDA files using both the DDA_LFQ and...
