BMSO search #136
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Hi, I would like to use xiSEARCH to analyze XL data obtained with the BMSO xlinker (ref). This xlinker exists in two forms, either as a closed-ring species with a succinimidyl moiety or as an open-ring species with a succinamic acid thioether moiety, so I have added both forms as idividual xliker with their stubs in the config file. Is it then correct to use the |
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Hi, Correct, you would use multiple crosslinkers the way you specified, giving them different names and using the deltamass of the species after reaction. I would also maybe suggest checking the TOPMATCHES option in a benchmarking/troubleshooting phase and setting that to False - you may want to have reported both explanations for a PSM and see if spectra can be explained by both the closed-ring and the open-ring. See the table here https://github.com/Rappsilber-Laboratory/XiSearch?tab=readme-ov-file#setting-up-a-search-in-the-advanced-interface-and-editing-config-files and look for TOPMATCHES. In the real analysis, you do want to set that to True as in a deposition/paper or for xiview you will likely want a single annotation per spectrum. |
Hi,
Correct, you would use multiple crosslinkers the way you specified, giving them different names and using the deltamass of the species after reaction.
I would also maybe suggest checking the TOPMATCHES option in a benchmarking/troubleshooting phase and setting that to False - you may want to have reported both explanations for a PSM and see if spectra can be explained by both the closed-ring and the open-ring. See the table here https://github.com/Rappsilber-Laboratory/XiSearch?tab=readme-ov-file#setting-up-a-search-in-the-advanced-interface-and-editing-config-files and look for TOPMATCHES.
In the real analysis, you do want to set that to True as in a deposition/paper or for xiview yo…