search

HUPO-PSI / mzTab

mzTab Reporting MS-based Proteomics and Metabolomics Results
https://hupo-psi.github.io/mzTab
37 stars 16 forks source link

SML best_id_confidence_measure (spec doc 6.3.12) #164

Open andrewrobertjones opened 5 years ago

andrewrobertjones commented 5 years ago

Relatively minor issue but seems possibly worth fixing, at least while the specs are under review. We are asking file producers to repeat a score type in this column of the SML table, yet they are also reported in the MTD section. It would seem better if we have just use integer codes to reference back to the measure used.

`

MTD id_confidence_measure[1] [MS,MS:1002889,Progenesis MetaScope Score,]
MTD id_confidence_measure[2] [,,Fragmentation Score,]
MTD id_confidence_measure[3] [,,Isotopic fit Score,]

` ...

` best_id_confidence_measure

[MS,MS:1002889,Progenesis MetaScope Score,] [MS,MS:1002889,Progenesis MetaScope Score,] [MS,MS:1002889,Progenesis MetaScope Score,] [MS,MS:1002889,Progenesis MetaScope Score,] `

Proposed model:

` best_id_confidence_measure

1 1 1 1 `

kayrein commented 5 years ago

Implementation in PR https://github.com/HUPO-PSI/mzTab/pull/168

nilshoffmann commented 5 years ago

@andrewrobertjones I would put this up for debate whether we want to fix this right now. The spec doc still has the CvParam version inside, the implementation following this "verbose" mode. Can we live with this for now and maybe want to revise this for 2.x? And the current example files all follow this old mode (minus the MTBLS263 one that I corrected in PR #170 )