The proteomics AWG subgroup have provided feedback on the sample and assay templates for proteomics.
@kristen.peach and @san-huei.laipolo please reply to this topic with any questions you have for the group about the proposed updates.
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:
I think that covers it 
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.
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,
Hi Proteomics AWG sub-group,
Kris populated the proteomics assay table for OSD-581 to the best of her ability and many of the columns requested by this group are blank.
Will you all please preview the protocol text and the assay table for this study using the following link: https://osdr.nasa.gov/bio/repo/data/studies/OSD-581/preview/7ardO8DK4k9gDOSjWR3g5AcTlzbhTllj.
Note that the info in the protocol text and the linked publication are all we have to go off of. If there is anything not noted in the publication or protocols that would be critical to processing, let Kris know and she’ll reach out to the submitter.
If there are any tips you all can add for how to know which file belongs in which column on the assay table, that would be very helpful.
As a reminder, the updated metadata template can be found here: Assay_Table_protein_expression_ms
@joel.steele @kristen.peach @hosseinvk @terry.lim @CoCo.Headley @spruce @nivedsanthosh99
Thank you for the summary Amanda! Anyone with feedback should feel free to reply here or email me at kristen.peach@nasa.gov
Hi Proteomics Sub-group Members,
Will you all please preview the updated protocol text and the assay table for OSD-581 using the following link: NASA OSDR: Open Science for Life in Space
There are several of the updated metadata fields and files missing (see list below). The info in the protocol text and the linked publication are all we have to go off of. Please add a comment with any of the missing metadata or files you are able to find in the protocol text or publication.
If there is any metadata not found in the publication or protocols that would be critical for processing, let Kris know and she’ll reach out to the submitter.
Also, if there are any tips you all can add for how to know which file belongs in which column on the assay table, that would be very helpful.
As a reminder, the updated metadata template can be found here: Assay_Table_protein_expression_ms
Missing metadata for OSD-581:
@mjr5770 @vinita.chauhan @sudip.sharma.temple @joel.steele @terry.lim @hosseinvk @mmarto3 @npelonis @alavia @parshawn @Mehwish @CoCo.Headley @cangercekk @sreev @Prisha_K @Meghana @spruce @nathaliepineda @nivedsanthosh99 @schandra @ccnaney @Gio04 @KariJ @yenkai.chen.id @amaanarif25 @Krishnan_Abhishek