bigbio / bigbio/quantms

Open-search with quantms, use cases and workflow

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#345 1 comment 0 reactions 1 assignee Claimed by @daichengxin View on GitHub
documentation enhancement high-priority open-search sage-support
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Description

### 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

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