Batoul Alallam The reference to the paper seems to have escaped:

Plant Cell. 2011 Jul; 23(7): 2477–2482.

doi: 10.1105/tpc.111.086272

PMCID: PMC3226225

PMID: 21771932

I confirm that the links to supplementary material don't work.

In my opinion, this paper doesn't entirely meet the requirements of the metabolomics community. In particular, the term "annotation" should surely indicate that when a metabolite - identified or not - is found again in a later study, there can be no doubt at all that the same compound has been detected.

By that definition, as proposed in particular for steroids by Shackleton's group (2010), it is rarely possible to annotate a metabolite using LC-MS, however elaborate the mass spectrometer may be.

I have discussed this question in two diatribes published on RG about the failure, during half a century, to identify a putative endogenous inhibitor of Na,K-ATPase:

Putative inhibitors of the sodium-potassium pump in mammals: a review. April 2018, DOI: 10.13140/RG.2.2.10992.35845

'Endogenous ouabain (EO)' in mammals: absence of valid experimental evidence. December 2019, DOI: 10.13140/RG.2.2.10144.53765

I cited an earlier article, which may be useful here:

Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, et al. Proposed minimum reporting standards for chemical analysis. Metabolomics 2007 Sep 19 ;3(3):211–21. DOI: 10.1007/s11306-007-0082-2

However, I consider that this important subject, which is as old as chemistry, ought to be a matter for learned societies, particularly our chemical societies.

Tuobang Li

Historically, the "fingerprint region" of IR spectra (1950s) brought a revolution in the way organic compounds were "annotated". This has never been practical for trace amounts when coupled on line with chromatography, which allows background subtraction. You can read a sense of frustration in the publications (1959-1960) on the first identification of melatonin, and on the most probably incorrect identification of L-rhamnose in a mammal (1961).

For a long time, GC-MS with electron ionisation was the only such method available (during the 1970s it was backed up by CI). Later, particle beam and moving belt LC interfaces were commercialised, though they were unpredictably insensitive and somewhat distained by theoreticians. However we used them in industrial applications such as pharmaceutical analysis because of the time they saved when they did work, for example in identifying a drug metabolite. Then there was a shortage of helium.

It doesn't seem unreasonable to envisage a way of obtaining high energy odd-electron ions from the low-energy even-electron ions obtained with current LC-MS instruments.