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

Polypropylene microcentrifuge tubes (MCTs) are increasingly used in lipidome sample preparation. In the absence of a comprehensive study evaluating ramifications of plasticware utilization in mass spectrometry-based lipidomic analyses, we conducted a systematic analysis to elucidate potential negative effects ascribable to labware contamination in serum lipidomics. During serum lipid extractions, tested glassware introduced 24 labware contaminants. In contrast, Eppendorf polypropylene MCTs contributed 485 contaminant features, many of which could be erroneously putatively identified as lipids via their m/z values. Eppendorf MCTs contamination engendered severe ion-suppression of 40 low abundance serum lipids, while generating mild to modest lipid ion-suppression across a multitude of higher abundance coeluting lipids. Less compatible polypropylene MCTs from an alternative manufacturer introduced a staggering 2,949 contaminant m/z values, severely affecting 75 coeluting serum lipids and causing more frequent and pronounced ion-suppression instances. Furthermore, by performing serum extractions with varied initial volumes, it was ascertained that labware-induced lipid ion-suppression is a dynamic phenomenon, contingent on both lipid and labware contaminant concentrations where low-abundance lipids are disproportionately impacted by coelutes of suppressive contaminants. In addition to lipid ion-suppression, the identification and quantification of 7 fatty acid endogenous serum lipids were compromised by the leaching of structurally identical surfactants from MCTs. MCTs artificially introduced 10 additional primary amides extraneous to serum samples. Utmost caution is imperative in interpreting data concerning primary amides and fatty acids when employing plastic labware. Through this investigation, we aspire to elevate awareness regarding the pernicious impact of labware contamination on lipidome analysis.