I am new to the metabolomics, and I used MZmine tool for analyzing the profile negative mode dataset from LC-MS.
While using this tool, there is a parameter (no ionization, M+H, M-H, etc.) in the online data search after alignment. However, searching in positive and negative mode gave the different results of a molecular compound.
Any suggestion is much appreciated.
Thanks a lot.
Mr. Singh,
There is not possible to obtain different result because of the MSs are they negative or positive reflect the energetics of a concrete molecule. But the ionization efficiency can be different and the fragent patterns as well. On this base there can be low intensive MS peaks which are not detected in the database due to low concentration of the analyte, for example (one possible reason). So the MS spectra should be at a set of different concentrations, temperatures and medium (solvent, solvent mixtures), including instrumental MS characteristics, etc., in order such as database to provide meaningful information.
In general, there is not recommendable to operate with databases of MS spetra. There should be applied the ISO procedures. MS measurements of the analyte compared with MS measurements of a standard compound in context intralaboratory variability of the obtained MS data.
Hello,
mzMine 2 has video: https://www.youtube.com/watch?v=VS_Zpyl5chQ
Huge documentations (PDFs of 100s of pages!): http://mzmine.github.io/documentation.html They also have a community/ forum.
The manuscript: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395 and https://www.ncbi.nlm.nih.gov/pubmed/28644610
Also, your questions shows lack of experience with mass spectrometry.
"You analyze the data in "x"-mode only if you have acquired the mass-spectrometry data in "x" mode"- where "x" is either Positive or Negative mode, but never both or interchangeably. Also, running conditions and molecules detected, their quantification all will be different for both modes, reflecting in different ions/ adducts- so you can not attempt what you are trying to do. Please consult a mass-spec person as a first hand information.
Thanks,
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