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compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
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opt parameter in config file #60

Closed MarcIsak closed 4 years ago

MarcIsak commented 4 years ago

Hi,

I'm taking a look at the config.txt file example in the repository here, and I noticed that all ptms have this opt parameter in between the mass shift and the AA residue regardless of whether they are fixed or variable like:

ptm=Oxidation,15.994915,opt,M ptm=Carbamidomethyl,57.021464,opt,C

I just would like to know what opt really means in this case? Can this opt be changed in any way? In case of the Carbamidomethylation, I would like to add it as a fixed ptm, but have the oxidation on M as a variable modification. How can this be setup?

Best,

Marc

RalfG commented 4 years ago

Hi Marc,

We share this config file with some other projects, which is why this field is present. In the case of MS²PIP, the opt/fix field it is not taken into account. Each modification needs to be listed in the modifications column next to the peptide in the peprec input file. So fixed modifications also need to be listed explicitly for each peptide. There is an example in the readme file.

If you start from a fasta file (using fasta2speclib), there's another config file where you can set the fixed/variable modification input: https://github.com/compomics/ms2pip_c/wiki/fasta2speclib

MarcIsak commented 4 years ago

Thanks, I think I understand now!

Best,

Marc