bigbio
Open-search with quantms, use cases and workflow
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:
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[ ] 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.
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[ ] 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.
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[ ] Use Percolator to boost the number of IDs based on open-search results.
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[ ] 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:
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[ ] 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.
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[ ] 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
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!
