Pre-processing liquid chromatography/high-resolution mass spectrometry data: extracting pure mass spectra by deconvolution from the invariance of isotopic distribution

RATIONALE Mass spectra obtained by deconvolution of liquid chromatography/high‐resolution mass spectrometry (LC/HRMS) data can be impaired by non‐informative mass‐over‐charge (m/z) channels. This impairment of mass spectra can have significant negative influence on further post‐processing, like quantification and identification. METHODS A metric derived from the knowledge of errors in isotopic distribution patterns, and quality of the signal within a pre‐defined mass chromatogram block, has been developed to pre‐select all informative m/z channels. RESULTS This procedure results in the clean‐up of deconvoluted mass spectra by maintaining the intensity counts from m/z channels that originate from a specific compound/molecular ion, for example, molecular ion, adducts, 13C‐isotopes, multiply charged ions and removing all m/z channels that are not related to the specific peak. The methodology has been successfully demonstrated for two sets of high‐resolution LC/MS data. CONCLUSIONS The approach described is therefore thought to be a useful tool in the automatic processing of LC/HRMS data. It clearly shows the advantages compared to other approaches like peak picking and de‐isotoping in the sense that all information is retained while non‐informative data is removed automatically. Copyright © 2013 John Wiley & Sons, Ltd.