Studies of Labware Contamination during Lipid Extraction in Mass Spectrometry-Based Lipidome Analysis

Abstract

In lipidomic analysis, plasticware is increasingly being used for lipid extraction and other sample processing procedures over glassware. However, a systematic investigation of the consequences of plasticware use on mass spectrometry (MS)-based lipidome analysis is lacking. In this work, we present an analytical approach for detecting and comparing solvent and labware contaminants encountered in lipidomic workflows. It is shown that the contaminant profiles varied widely between microcentrifuge tubes from different manufacturers. The most suitable polypropylene tubes tested introduced 847 labware-originating contaminant m/z's when three different manufacturing batches were tested for Folch lipid extractions. Of particular concern is that 21 primary amide and fatty acid surfactants were introduced that were identical to biological endogenous lipids, 16 of which had not been previously reported as leachables from polypropylene materials. Alternatively, the use of borosilicate glassware and PTFE-lined screw caps introduced 98 different contaminant m/z's across three manufacturing batches tested for Folch extractions. Despite the overwhelming number of labware contaminants introduced, current databases and literature only facilitated the identification of 32 contaminants. To address the dearth of publicly available contaminant information, we provide a comprehensive labware contamination repository containing high-resolution m/z values, adductation information, retention times, and MS/MS spectra. This resource should prove to be valuable for researchers in detecting and distinguishing contaminants from analytes of interest. A companion paper presents a detailed study of how labware contamination can lead to ion-suppression effects on coeluting lipids and interference in the analysis of endogenous lipids, such as those from human sera.

Investigation of the Effects of Labware Contamination on Mass Spectrometry-Based Human Serum Lipidome Analysis

“…However, the ionization responses of these surfactants may differ from their respective normalizing signals of FA 18:0 and NAH 18:1, rendering the reported values as approximations. Moreover, the significant interbatch variance of these contaminants, as reported in the cosubmitted manuscript, may further diminish the utility of the provided values. The multifarious origins of erucamide (NAH 22:1) contamination and current Eppendorf surfactant contamination are discussed in Supplemental Note S5.3.…”

“…Additionally, 40 other contaminant features (from 36 distinct contaminants) were detected within the same elution time frame, tabulated in Supplemental Table S5. For structurally unidentified contaminants, pertinent experimental data and the unique labware contaminant ID #’s introduced in the cosubmitted manuscript are included …”

“…Among the different types of contaminants found, plastic-leached primary amide (NAH) and fatty acid (FA) surfactant contamination is particularly troublesome since they are identical to endogenous lipids . These constitute biologically pertinent molecules endowed with critical physiological functions. , …”

“…These solvents readily dissolve and extract an array of compounds upon contact with labware. In our earlier work cosubmitted with this submission, we detailed a comprehensive methodology for detection, identification and comparative analysis of contaminants originating from various types of labware routinely employed in lipidomic workflows . Notably, the use of polypropylene resulted in pronounced mass spectral contamination, with the extent of contamination varying significantly among ostensibly similar polypropylene microcentrifuge tubes (MCTs) from different vendors tested.…”

“…Complementing to our earlier work of detecting and identifying labware contaminants, the objective of this study is to explore challenges and methodological intricacies introduced by the spectrum of labware contaminants, including ion suppression effects, in the precise identification and quantification of lipids extracted using the Folch method. Given the widespread application of serum lipidomics in biomarker discovery for various disease phenotypes, − we opted to utilize human serum samples as the biological matrix template to evaluate the potential adverse effects of labware contaminants.…”