FragPipe

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Philosopher 4.1.1 generates empty files due to the incompatibility of the fasta file

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Dear developer team, I am trying to use the fasta database generated in this paper: https://www.nature.com/articles/s41587-021-01021-3. In brief the new fasta file has additional~320K proteins resulted from different RNA sequencing...

fazeliniah

The same protein group has different protein IDs in protein.tsv files from different experiments

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- Describe the issue or question: Hi, I am trying to quantitate a group of timsTof dda experiments using ionQuant and close to end of the process I got an...

jd690764

There are high probability peptides being filtered out after protein assignment.

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Hi Fengchao, Wish you are having a great holiday! So, I've been trying to import interact -.xml files generated from MSFragger-DIA + DDA(DIA_Speclib_Quant workflow) into Skyline and to generate a...

weixiandeng

Philosopher error: panic: runtime error: index out of range [2723] with length 2723

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Hi Team Fragpipe, I've recently updated to Fragpipe V17.0, where I try to use "DIA_Speclib_Quant" workflow. in this case, I just want the library.tsv file. There seems to be some...

PatrickvanZalm

Let Philosopher print errors when there are protein hits from PSMs that cannot be found in the fasta file.

1

This is a bug/feature I found by accident (https://github.com/Nesvilab/FragPipe/issues/537#issuecomment-995943414). Basically, when you search the data with FASTA file A, and run Philosopher to filter the result using FASTA file B,...

fcyu

FragPipe for middle-down search

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Hello, I wonder if FragPipe could be tuned to work as a middle-down search engine. It is a very fast tool, I can handle a nonspecific search of peptides in...

Apirog9

Number of TMT-integrator-summarized peptides is only 10% of identifications from proteogenomics database

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Dear FragPipe team, I am working with a phenotype-specific proteogenomic database created using a customized Galaxy pipeline for fetching SRA RNAseq data, genome mapping, variant calling, and database creation with...

MiguelCos

Mismatched data in MSFRagger results files

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Hello I have been analyzing MS data after using FragPipe version 16.0/MSFragger version 3.3/Philosopher version 4.0.0 (build 1626989421) and have noticed some mis-matching data in the results files as listed...

treponeme

msstatsTMT

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- Describe the issue or question: Question: For label-free data, fragpipe offers to export MSSTATS compatible output ( which is really awesome ). Do you think you could also support...

KlemensFroehlich

Quesions for glycan workflows

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Hi Fragpipe I’m unsure of where to ask this question, so I’ll drop it here… If you prefer to take it by mail or something else, let me know and...

MNTsnowman