Suggestions to SDRF v1.1.0

[jonasscheid]

I really like the addition of subdomain-specific templates! Feedback on what I think would be still great to have in SDRF 1.1.0:

• Allow multiple —templates separated by , e.g. immunopeptidomics,dda-ms-proteomics to validate against
• Add functionality that generates an header-only tsv file based on the --template flag that the user can fill
• Data-dependent acquisition (DDA) Template addition request (optional columns):
  • comment[precursor mass tolerance]
  • comment[fragment mass tolerance]
  • comment[digest mass range]
  • comment[prec charge]

@ypriverol @timosachsenberg

[ypriverol]

Thanks a lot for your comments, I will add them to the specification, great catch. Was wondering how you use:

• comment[digest mass range]
• comment[prec charge]

[timosachsenberg]

Probably set in the instrument software? Then maybe it is an acquisition parameter?

[jonasscheid]

I would parse those directly into Comet. You can also rename e.g. to more verbose comment[precursor charge range] or comment[precursor mass range]

Example:

• comment[precursor charge range]: '1:3'
• comment[precursor mass range]: '800:5000'

Also precursor range and mass window you often need to define in the MS method, so not only a search parameter