Connecting RAMclustR with MetFamily

[sneumann]

Hi, it would be great to have a working example snippet on how to connect RAMclustR output to MetFamily.

What we need is an MSP file that looks like this: https://raw.githubusercontent.com/ipb-halle/MetFamily/master/files/MSMS_library_showcase.msp

NAME: Unknown
RETENTIONTIME: 8.4209
PRECURSORMZ: 85.00465
METABOLITENAME: 
ADDUCTIONNAME: [M-H]-
Num Peaks: 3
75.00941    44.5240135192871
79.95998    54.568229675293
85.00496    297.418823242188

i.e. where we have RT and Precursor that can be matched to the MS1 precursor.

Then we need the MS1 quantification as it comes from XCMS, looking like https://github.com/ipb-halle/MetFamily/blob/master/files/Metabolite_profile_showcase.txt Full spec of the MetFamily input formats are in https://github.com/ipb-halle/MetFamily/blob/master/files/MetFamily_Input_Specification.pdf

@Treutler and @cbroeckl , is there a way to create a small HowTo (some people at UC RIverside would love to see that ...) so we can include that in RAMclustR documentation ?

@cbroeckl , is the file https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/spectra/test.mspLib what the RAMclustR output looks like ? It has the RT in a comment tag.

Yours, Steffen

[cbroeckl]

I am writing .msp format currently for spectra without precursor selection. I also have output formats including .ms and .mat (Sirius and MSFinder) - each of these is similar to .msp, but not identical. Before we get too far into the msp format (which I should be able to do pretty easily) we should make sure it is valid. Last I checked NIST had no definition for RETENTIONTIME - but this was a while ago and I can't say I am current on that. Can you send a document you are referring to for valid NIST line headers?
Thanks, Corey

[cbroeckl]

see here for my reference:
https://www.nist.gov/sites/default/files/documents/srd/NIST1aVer22Man.pdf I have always reverted to the NIST definitions of msp format. Maybe there is something more recent, but you can see on page 68 that retention time isn't listed (though retention index is). There is a better document for defining acceptable fields out there, but I can't find anything on the NIST site due to the US govt shutdown....

[Treutler]

The msp format accepted by MetFamily is used at RIKEN and is not identical to the NIST msp format. Please find an example above. It would be great to have this output from RAMClustR. Please let me know if I can help with the MetFamily integration.

[hechth]

@Treutler actually matchms will be expanded to allow conversion between NIST and RIKEN format.

[hechth]

@sneumann is this still up to date or has this been resolved? If you're still interested in this we could start tackling this at some point.