This question has to do with how to mark up a consensus spectrum to link it back to the replicating spectra in their raw files when those raw files aren't on ProteomeExchange.
Mapping AAAQWVR/2 to many, many spectra across multiple raw files. The appropriate way to express this (so far as I can tell) is to use either contributing replicate spectrum keys or contributing replicate spectrum USI. The second option makes sense since those contributing spectra aren't in the library itself. However, this project didn't publish its data on ProteomeExchange so I cannot construct a "real" USI for it.
Options
Fake USI
This looks "okay" and preserves the available information, but feels wrong because it sets up an expectation that this URI resolves to something. If there were a way to canonically express that this is a "local" or "private" dataset in the accession field, that would make this less misleading.
This looks better as written, though it isn't preferable since A) it's more verbose, B) is universally not portable, and C) it conflicts with the usage of scan number and constituent spectrum file as used for individual spectra where they are not grouped.
This question has to do with how to mark up a consensus spectrum to link it back to the replicating spectra in their raw files when those raw files aren't on ProteomeExchange.
Files
Spectrum Library: https://chemdata.nist.gov/download/peptide_library/libraries/skin_hair/IARPA3_best_tissue_add_info.msp.zip
Metadata File: https://chemdata.nist.gov/download/peptide_library/libraries/skin_hair/IARPA3_all.out.zip
Metadata is a sparse table mapping consensus spectra to their contributing replicates:
Mapping
AAAQWVR/2
to many, many spectra across multiple raw files. The appropriate way to express this (so far as I can tell) is to use eithercontributing replicate spectrum keys
orcontributing replicate spectrum USI
. The second option makes sense since those contributing spectra aren't in the library itself. However, this project didn't publish its data on ProteomeExchange so I cannot construct a "real" USI for it.Options
Fake USI
This looks "okay" and preserves the available information, but feels wrong because it sets up an expectation that this URI resolves to something. If there were a way to canonically express that this is a "local" or "private" dataset in the accession field, that would make this less misleading.
Attribute Groups
This looks better as written, though it isn't preferable since A) it's more verbose, B) is universally not portable, and C) it conflicts with the usage of
scan number
andconstituent spectrum file
as used for individual spectra where they are not grouped.