How to identify unknown compound by the chromatogram and peaks received by MALDI-ToF
I am assuming that the unknown compound is an unknown protein. Depending on molecule and ionization technique you could be looking at quasimolecular ions such as [M+H]+ or [M+2H]2+ (from e.g. ESI), or M+. (from Electron Impact, EI). Do you happen to have MZ, mzXML files?
If you are using .RAW file, Then it could be better to use MSconvert to convert your raw to mzxml / mzml / mgf file format. Those files are the commonly accepted format for most of the search engine nowadays. Sure this will help you to search your protein easily using any Search engine.
Later you can use a freely available Search engine like MS-GF+, mMASS, Morpheus etc. I could suggest you use Morpheus as its very easy to use for the beginners with good output result.
Ping me if you need any help
Very little info in this question.
Generally:
- If this is an intact protein, it is impossible, unless you only have a few candidates to choose between.
- Peptides coming from a single protein (it may also work for two or max three proteins), generated by using trypsin or other proteases with known specificity: Use webtools to search in protein databases, for example MS-Fit in the ProteinProspector suite ( http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msfitstandard ) or Matrix Mascot's Peptde Mass Fingerprint ( http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=PMF ). Both work in essentially the same way.
-If this is a smaller molecule, like a metabolite, it is again close to impossible, as you probably only have the m/z of the intact molecule, and not for any fragments. If it is a really good MALDI-TOF instrument, you may approach the chemical formula by analyzing the peak heights together with the m/z value. But if you have some knowledge about fragments, you may try METLIN ( https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage# )
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