Open-search with quantms, use cases and workflow

[ypriverol]

Description of feature

@daichengxin #contributors

With the support of SAGE by quantms, we have opened the possibility to support a quantms open-search workflow. I recommend the following steps:

• Implement an identification workflow based on SAGE enabling open-search analyses. I think we don't have to implement the quantification part in the first iteration because mainly research in open-search analyses are id-based.

• Implement a Python tool that enables to analyse the delta masses and identified the potential modifications for each delta mass. The use cases for this tool are:

  • Glycoproteomics
  • Additional post-translational modifications for proteogenomics validation. Given an MGF or mzML files find with open-search all the spectrum that could be identified which will be potential FP Identifications in variants.

• Use Percolator to boost the number of IDs based on open-search results.

• We may need to support other files such as MGF files because in proteogenomics you may have a single file with the spectra for all novel peptides.
  This is the first issue about this topic, and It will be good to see before starting coding the following challenges:

• See if other tools and packages can be used to perform the identification of the Mods on delta masses, which means we don't need to implement the Python tool.

• See if SAGE team @lazear if not working on a similar tool, coordinate with him this development.

Please feel free to give us feedback @timosachsenberg @jpfeuffer @fabianegli @WangHong007

[lazear]

One option is to shim Sage outputs into a format that PTM-shepherd use:s https://github.com/Nesvilab/PTM-Shepherd

I submitted a grant to the CZI open source program for Sage, and one of the aims is to develop/integrate some open search refinement tools, so let's hope it gets funded!