Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis

Abstract

Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise the data quality and can damage the chromatography and mass spectrometry instruments. However, researchers may not discover contamination issues until after data acquisition. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and low-cost contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in MS sample preparation workflow. Only one microliter of sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom- up proteomic methods, regarding the effectiveness of removing detergents, peptide recovery, and reproducibility. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. ContamSPOT can also provide a unique readout of sample cleanness for developing and evaluating MS-based sample preparation methods. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers. Table of Contents (TOC) graphic(All images used in the TOC graphic are original, in compliance with copyright guidelines.) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/574392v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@7b6f0aorg.highwire.dtl.DTLVardef@1b6fcd9org.highwire.dtl.DTLVardef@9213a5org.highwire.dtl.DTLVardef@47b7fb_HPS_FORMAT_FIGEXP M_FIG C_FIG