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Score becomes 0 if no MS2 peaklist information provide. #25

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fxd1106 opened this issue Jun 21, 2019 · 2 comments

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@fxd1106
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commented Jun 21, 2019

Hi,
We have generated a dataset with only MS1, when I try to perform the database searching without MS2, all the probabilistic scores become 0. How can we deal with this issue?

@schymane

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commented Jun 21, 2019

The MetFrag scoring function needs fragments (MS2) to come up with a score above zero. If you do not have any fragmentation data, then you can only use additional metadata (literature, patent counts, etc) to score your candidates. If you are using PubChem, then you can retrieve this additional data and add it as a score on the "Candidate Filter and Scoring Settings" tab. There you will also find other available options to score your candidates. But please do bear in mind that most additional scores are not based on experimental data then, so e.g. the ranking based on patent and literature counts may not always make sense in terms of your experimental context.

@schymane

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commented Jun 21, 2019

https://msbi.ipb-halle.de/MetFrag/
and
https://github.com/schymane/ReSOLUTION
have more information on scoring functions.
ReSOLUTION still needs a peak list to run, but you can set a dummy MS/MS file of mz 999 and int 999 so that the fragmenter score is always zero, but other metadata scores can be used.

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