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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.
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!
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:
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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