A batch correction method for liquid chromatography–mass spectrometry data that does not depend on quality control samples

Martin James Rusilowicz, Michael Dickenson, Adrian Charlton, Simon O'Keefe, Julie C. Wilson

Research output: Contribution to journalArticlepeer-review


The need for reproducible and comparable
results is of increasing importance in non-targeted metabolomic
studies, especially when differences between
experimental groups are small. Liquid chromatography–
mass spectrometry spectra are often acquired batch-wise so
that necessary calibrations and cleaning of the instrument
can take place. However this may introduce further sources
of variation, such as differences in the conditions under
which the acquisition of individual batches is performed.
Quality control (QC) samples are frequently employed as a
means of both judging and correcting this variation. Here
we show that the use of QC samples can lead to problems.
The non-linearity of the response can result in substantial
differences between the recorded intensities of the QCs and
experimental samples, making the required adjustment
difficult to predict. Furthermore, changes in the response
profile between one QC interspersion and the next cannot
be accounted for and QC based correction can actually
exacerbate the problems by introducing artificial differences.
‘‘Background correction’’ methods utilise all
experimental samples to estimate the variation over time
rather than relying on the QC samples alone. We compare
non-QC correction methods with standard QC correction
and demonstrate their success in reducing differences
between replicate samples and their potential to highlight
differences between experimental groups previously hidden
by instrumental variation.
Original languageEnglish
Number of pages12
Issue number56
Publication statusPublished - 18 Feb 2016

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