Journal of The American Society for Mass Spectrometry

, Volume 30, Issue 9, pp 1733–1741 | Cite as

Mass Accuracy Check Using Common Background Peaks for Improving Metabolome Data Quality in Chemical Isotope Labeling LC-MS

  • Yunong Li
  • Liang LiEmail author
Research Article


Chemical isotope labeling (CIL) LC-MS is a highly sensitive and quantitative method for metabolome analysis. Because of a large number of peaks detectable in a sample and the need of running many samples in a metabolomics project, any significant change in mass measurement accuracy during the whole period of running samples can adversely affect the downstream peak alignment and quantitative analysis. Herein, we report a rapid method to check the mass accuracy of individual spectra in each CIL LC-MS run in order to flag up any run containing spectra with accuracy drift that falls outside the expected error. The flagged run may be re-run or discarded before merging with other runs for peak alignment and analysis. This method is based on the observation that some background signals are commonly detected in almost all spectra collected in CIL LC-MS runs. A mass accuracy check (MAC) software program has been developed to first find the common background mass peaks and then use them as mass references to calculate any mass shifts over the course of multiple sample runs. Using a metabolome dataset of 324 human cerebrospinal fluid (CSF) samples and 35 quality control (QC) samples produced by CIL LC-MS, we show that this accuracy check method can streamline the initial raw data processing for downstream analysis in metabolomics.


Chemical isotope labeling LC-MS Mass accuracy Peak alignment Metabolome analysis Metabolomics 



This work was supported by the Natural Sciences and Engineering Research Council of Canada, CIHR, Canada Research Chairs, Canada Foundation of Innovations, Genome Canada and Alberta Innovates. We thank Ms. Xinyun Gu for providing the CSF data.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no competing interest.

Supplementary material

13361_2019_2248_MOESM1_ESM.pdf (187 kb)
ESM 1 (PDF 186 kb)
13361_2019_2248_MOESM2_ESM.pdf (31 kb)
ESM 2 (PDF 31 kb)


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Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of AlbertaEdmontonCanada

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