Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross‐platform transferable chemical signatures

Abstract

RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different LC-MS platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC-MS platforms using reversed phase chromatography and different chromatographic scales (nano, conventional and UHPLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (RSD < 2%); however, substantial differences were found in the LC-MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable.

Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS

“…LC-MS is currently the method of choice for global metabolomics studies because it provides the highest metabolite coverage using a single analytical technique2. Typically, several hundred to thousand(s) metabolites can be detected in a single analysis3. The size of human metabolome is currently unknown, but is projected to exceed the conservative estimate of 4229 endogenous metabolites in concentrations spanning 11 orders of magnitude4.…”

Concurrent profiling of polar metabolites and lipids in human plasma using HILIC-FTMS

“…Therefore, metabolite profiling of blood samples has been widely used in biomarker discovery67891011 and assessments of adverse outcome pathways (AOPs) induced by chemicals12, drugs131415 and environmental stress16. Liquid chromatography coupled with mass spectrometry (LC-MS) is one of the main techniques for blood plasma metabolite profiling171819. To date, many of these studies focused on either the polar metabolite2021 or lipid fractions6222324.…”

“…Reversed phase liquid chromatography (RPLC) is the most popularly used separation method1819. However, polar and ionic metabolites, such as organic acids and amino acids, are not suitable to analyze with RPLC because they exhibit low hydrophobicity, which leads to weak interaction with stationary phase, poor retention and separation in RPLC mode1937.…”

LC–MS based global metabolite profiling: the necessity of high data quality

“…A possible route towards distinguishing between analytical and biological variation is the use of the previously mentioned plasma-based SRM 1950 as described by the qualitative metabolomics cross-platform profiling report by Simón-Manso et al (Simón-Manso et al 2013). This reference standard could therefore be used to explore analytical aspects of data quality such as reproducibility, batch-tobatch variations and foremost to enable reliable interlaboratory comparisons based on a well-characterized standard (Telu et al 2016).…”

“…Sampling and sample preparation as well as the method used during LC-MS analysis have a profound effect on the likelihood of generating analytically reliable hypotheses (Gika et al 2014a, b;Vuckovic 2012). A number of publications has focused on assessing and measuring data quality for global metabolite profiling (Gika et al 2016;Naz et al 2014;Naz et al 2013a;Naz et al 2013b;Pandher et al 2009;Simón-Manso et al 2013;Telu et al 2016;Tulipani et al 2013Tulipani et al , 2015Whiley et al 2012), however most of these only focus on a particular step in the workflow.…”