I have retrieved some full-scan ms chromatography data. I wish to look for one (potentially existing) specific compound. We already have the molecular structure and literature on the mass spetrum of this compound. The chromatographic elution time is not known, i.e. no pure standard substance is available. I guess I can locate this compound in the chromatographs by some matching algorithm, but have no clue on what software package to adopt.
As the mixture subject to analysis is complex, comaring the spectra peak by peak with human vision is not adequate.
Please recomend either small utility programmes or integrated lab suits. And, what have been done with the reverse lookup-by-compound method by people?
-- notes --
My absciex-analyst1.6.1 software doesn't seem to provide such option (correct me if I'm wrong). An approach may be look up all peaks against a home made database consisting of only one candidate entry, but this sound strange to me, as meaning of proximity don't work the other way around.
If I happen to write my own code, what probability-statistic framework is a good standing point?
If you have a ms spectrum (at least on paper, as you state) of your substance, proceed by extracting some selected m/z chromatograms for the main characterizing fragments: you should look for a chromatographic peak that has the same RT for all the selected m/z and corresponding abundances - by extracting the background subtracted spectrum at the RT you should have a spectrum to compare with the literature one - it's easier to do than to explain !
Alternatively, you can take a look at the AMDIS software deconvolution program from NIST (free) and, yes, in that case you have to build a one spectrum library. AMDIS scientific explanation is an excellentstarting point if you are committed to develop your own approach to software deconvolution.
hye sir Salvatore. Im interesting to know further by mean on development the spectrum library. Did u have any suggested references for me? thank.
Did you use GC MS (EI, CI ?) or LC MS (LC Qtof MS) using ESI, APCI or others?) By doing this I think you can have (HR) MS (and MS MS) data of certain peaks of your TIC. If you have (ESI) HR MS, you can have molecule formula after evaluating the isotopic pattern and accurate mass; after you predict molecule formula you can search in some online data base (e.g Metlin, Mass bank etc), by comparing the data of your compound and its fragmentation, and the data and its fragmentation (in data base), you may predict your compound. If you have EI MS you can compare with the data base in your GCMS (if any) or by ADMIS and NIST as described above, or other data base.
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