Proteomics AWG Subgroup - Metadata Templates

OSDR Feedback Submission/Curation Question?
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The proteomics AWG subgroup have provided feedback on the sample and assay templates for proteomics.

  • Columns that currently exist are in blue and proposed updates are in red text
  • New proposed columns are in yellow
  • An example row was added to each template

Sample Table

Assay Table

@kristen.peach and @san-huei.laipolo please reply to this topic with any questions you have for the group about the proposed updates.

@joel.steele @spruce

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I propose in the assay table: that the below column be re-labelled to be Channel (This covers all ratios etc) this is the most apt
m/z ratio (Da)
Reporter ion mass, m/z ratio (e.g. iTRAQ 114, 116, 118; TMT 126, 127, 128, 129, 130, 131; etc.). If we call this parameter a ‘ratio’ we ought to be reporting a ratio so I would like to propose a change here (even if this is a well understood norm in proteomics). Would ‘reporter ion intensity’ (http://purl.obolibrary.org/obo/MS_1001847, defined as: Intensity of MS2 reporter ion (e.g. iTraq).) work here? Or ‘reporter ion mass’?

Next, in addition to the below columns, I do believe there are some that should be accounted for:

Derived Spectral Data File
Peptide Assignment File
Protein Assignment File
Post-Translational Modification Assignment File

Additions:

  • Project specific study result file:
  • .pd, .pdsty, folder, (there are several other types)-
  • Refined Identification file:
  • .MzIdentml, .pepxml, .idp, paraquet-
  • Standardised file meeting proteomics standards
  • .sdrf or as above refined identification file-
  • Spectral Library:
  • Name of library file
  • Quant file:
  • Ion quant, fragments, precursors
  • Stripped peptide Sequences
  • Modified peptide
  • Fasta file used

I think that covers it :slight_smile:

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I think @joel.steele may have done me a favor and copied over some of my questions from the google sheet , thank you! My name is Kris Peach and I am the Curation Lead at OSDR. My questions for the group are in red font in the document in the following columns, m/z ratio (as joel alluded to), chromatography, detector, and analyzer. Please either tag me in the google sheet or here in the forum if you’d like to discuss my questions or suggestions.

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Hi Kris,

Pleasure to meet you, I will have a look now, apologies for the delay it is a very busy time of year

kindest regards,

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