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HUPO-PSI / proxi-schemas

ProXI: Schema definitions for the Proteomics eXpression Interface
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PRIDE PROXI spectra returning mzs not in order #73

Open edeutsch opened 3 years ago

edeutsch commented 3 years ago

Fetching a spectrum from PRIDE via PROXI such as: http://wwwdev.ebi.ac.uk/pride/proxi/archive/v0.1/spectra?resultType=full&usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_12_5Feb12_Cougar_11-10-11.mzML:scan:11850:[UNIMOD:214]YYWGGLYSWDMSK[UNIMOD:214]/2

returns the mzs in random order. This is not against the current spec, which does not specify. But it is breaking the Lorikeet viewer at ProteomeCentral. Seems like many applications may assume mzs in order.

What should be the resolution?

Does the random order of mzs at PRIDE match the same order of intensities? One risk of separate arrays is that they become unaligned.

ypriverol commented 3 years ago

Fetching a spectrum from PRIDE via PROXI such as: http://wwwdev.ebi.ac.uk/pride/proxi/archive/v0.1/spectra?resultType=full&usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_12_5Feb12_Cougar_11-10-11.mzML:scan:11850:[UNIMOD:214]YYWGGLYSWDMSK[UNIMOD:214]/2

returns the mzs in random order. This is not against the current spec, which does not specify. But it is breaking the Lorikeet viewer at ProteomeCentral. Seems like many applications may assume mzs in order.

What should be the resolution?

sorting is fine!!!

  • Should we update the documentation to allow mzs in any order? Write some code to compensate for out of order mzs in ProteomeCentral and all other applications?
  • Should we update the documentation to require mzs in ascending order? And update the PRIDE implementation?

If we decided the do it in that way we can change our implementation.

Does the random order of mzs at PRIDE match the same order of intensities? One risk of separate arrays is that they become unaligned.

@edeutsch as far as I know they match the intensities.

edeutsch commented 3 years ago

@ypriverol, what do you mean by "sorting is fine!!!"?

Will PRIDE start returning sorted mzs?

ypriverol commented 3 years ago

@edeutsch it means that what ever we decided we can implemented.