Highly multiplexed targeted plasma proteomics quantifies several hundred blood proteins in serum from colorectal carcinoma patients

Abstract

The rapid analysis of human serum and plasma can provide deep insights into changes of the blood proteome in response to different patient treatments or diseases. Targeted proteomics techniques, like SRM and PRM, can be utilized to monitor proteins at high sensitivitym but so far were limited to smaller protein panels, which can be monitored in one experiment. The recently, on a Bruker tims-TOF pro mass spectrometer, developed parallel reaction monitoring-parallel accumulation - serial fragmentation (prm-PASEF) method expands the standard PRM method by using ion-mobility. The use of ion mobility as a fourth separation dimension increases the proteome coverage while reducing the length of the necessary chromatogeaphic separation. By combining an isotope-labeled reference standard, which covers 579 plasma proteins, we were able to quantify 565 proteins in plasma using prm-PASEF, with the least abundant protein being quantified at 7 amol. We continued the analysis by combining the isotype-labeled reference standard with dia-PASEF, which allowed the quantification of 549 proteins. Both methods were used to analyze 20 patient plasma samples from a colorectal cancer (CRC) cohort. The analysis identified 16 differentially regulated proteins between the CRC patient and control individual plasma samples. 15 of the 16 proteins showed a high correlation to the mRNA expression in CRC tumor samples, showing the technique s potential for the rapid identification of potential biomarkers in larger cohorts, abolishing the need for preselection of potential biomarker proteins. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/486663v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@eda5d4org.highwire.dtl.DTLVardef@220b01org.highwire.dtl.DTLVardef@1008757org.highwire.dtl.DTLVardef@1b56665_HPS_FORMAT_FIGEXP M_FIG C_FIG