FragPipe

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Feature request: Add Normics normalization as an alternative to MaxLFQ?

3

A new data normalization method was recently published. It seems to be more robust than MaxLFQ according to this publication. "Normics: Proteomic Normalization by Variance and Data-Inherent Correlation Structure" https://doi.org/10.1016/j.mcpro.2022.100269

bhampton-som

Dear FragPipe Team, **Is your feature request related to a problem?** The requested feature is only for convenience. Currently the psm.tsv, ion.tsv, and peptide.tsv tables (and the combined versions of...

hollenstein

Wrong peptide start and end positions

1

Dear FragPipe Team, First of all, thank you very much for providing these fantastic tools. I am working at a proteomics MS facility and we are planning to switch to...

hollenstein

EasyPQP convert KeyError

8

Hi, I'm trying to build a spectral library from fractionated DDA data. I spiked in Pierce retention time peptides for each fraction and followed https://github.com/Nesvilab/FragPipe/issues/506 to search for my spike-in...

owentsai

Some proteins appearing in protein file but not peptide file

60

**Describe the bug** In my output files, the protein.tsv file contains some proteins that are not present in the peptide.tsv file or the [filename].tsv file. Can you explain to me...

ndtivendale

contaminants filtered from TMT-Integrator

5

I have noticed that FragPipe v.18 removes contaminant proteins from the outputs in the TMT-report folder, whereas they were kept in FragPIpe v.17.1. I am using a bovine casein spike-in,...

mwfoster

Feature request - associate diagnostic ions with particular PTMs

1

Hi all, Big fan of MS-Fragger and starting to try it out for various PTM-enriched searches. For some of the data sets I want to search, there are known diagnostic...

andrewrobertjones

Phosphopeptide site localization and quantification question

24

Hello, I am performing phosphoproteome-based closed searches with LFQ and have a question/clarification about the PTMProphet output. I appreciate the report format as it provides indexed and localized sites with...

enonimos

Can you add iTraq8 workflow to Fragpipe?

2

Hello, Can you please add iTraq8 workflow for timsTOF Pro data to Fragpipe? Thanks, TN

tnguyenwi

Increase number of peptides needed for Quant

8

Hi, We're analysing some bacterial proteome data between a mutant and wildtype strain on FragPipe v18 and we're having an issue with a protein being quantified in the mutant strain...

JLewisMicro