Converting to Input Files for CurtainPTM

Many program have different output format that CurtainPTM by default does not accept. This page will show you how to convert a selection of searched data format to CurtainPTM compatible input. We will mostly focus on the differential analysis files.

Requirements

Python 3.9 or above
curtainutils package

Installation

pip install curtainutils

MSFragger PTM single site output to CurtainPTM input

Ensure that your MSFragger PTM single site output file with differential analysis result has the following columns:

Index column containing the unique identifier for each ptm site that should also contain the uniprot accession id. If it does not have accession id, you will have to supply the script a fasta database that was used for the search.
Peptide column containing the peptide sequence.

Without fasta database:

msf-curtainptm -f <MSFragger PTM single site output file> -i <index column with site information> -o <output file> -p <peptide column>

With fasta database:

msf-curtainptm -f <MSFragger PTM single site output file> -i <index column with site information> -o <output file> -p <peptide column> -a <fasta file> 

Convert DIA-NN PTM output to CurtainPTM input

Ensure that your DIA-NN PTM output file with differential analysis result has the following columns from the pr report file:

Modified.Sequence column containing the peptide sequence with the modification site.
Precursor.Id column containing the precursor fragment.
Protein.Group column containing the protein.
PTM.Site.Confidence column containing the probability of the modification site.

diann-curtainptm -p <differential analysis file> -r <report file> -o <output file> -m <modification_of_interests from the Modified.Sequence column>

Convert Spectronaut output to CurtainPTM input

Ensure that your Spectronaut output file with differential analysis result has the following columns:

PTM_collapse_key column containing the unique identifier and modification site information.
PEP.StrippedSequence column containing the peptide sequence without modification.

spn-curtainptm -f <differential analysis file> -o <output file>

Last modified: 13 January 2024