CRC; DIA; PASEF; PRM; SIL peptides; biomarker; colorectal cancer; plasma; targeted proteomics; Peptides; Proteome; Blood Proteins; Humans; Mass Spectrometry/methods; Chromatography, Liquid; Proteomics/methods; Peptides/analysis; Mass Spectrometry; Proteomics; Chemistry (all); Biochemistry; General Chemistry
Abstract :
[en] Blood analysis is one of the foundations of clinical diagnostics. In recent years, the analysis of proteins in blood samples by mass spectrometry has taken a jump forward in terms of sensitivity and the number of identified proteins. The recent development of parallel reaction monitoring with parallel accumulation and serial fragmentation (prm-PASEF) combines ion mobility as an additional separation dimension. This increases the proteome coverage while allowing the use of shorter chromatographic gradients. To demonstrate the method's full potential, we used an isotope-labeled synthetic peptide mix of 782 peptides, derived from 579 plasma proteins, spiked into blood plasma samples with a prm-PASEF measurement allowing the quantification of 565 plasma proteins by targeted proteomics. As a less time-consuming alternative to the prm-PASEF method, we describe guided data independent acquisition (dia)-PASEF (g-dia-PASEF) and compare its application to prm-PASEF for measuring blood plasma. To demonstrate both methods' performance in clinical samples, 20 patient plasma samples from a colorectal cancer (CRC) cohort were analyzed. The analysis identified 14 differentially regulated proteins between the CRC patient and control individual plasma samples. This shows the technique's potential for the rapid and unbiased screening of blood proteins, abolishing the need for the preselection of potential biomarker proteins.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Lesur, Antoine; Luxembourg Institute of Health, Strassen L-1445, Luxembourg
Bernardin, François; Luxembourg Institute of Health, Strassen L-1445, Luxembourg
KONCINA, Eric ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
LETELLIER, Elisabeth ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
Kruppa, Gary; Bruker Daltonics, Billerica, Massachusetts 01821, United States
Schmit, Pierre-Olivier; Bruker Daltonique S.A., Wissembourg F-67160, France
DITTMAR, Gunnar ; Luxembourg Institute of Health, Strassen L-1445, Luxembourg
External co-authors :
yes
Language :
English
Title :
Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics.
We thank the Foundation Cancer for the support with grant FC/2022/01 SOCS to E.L. The authors would like to thank Dr. Guy Berchem and Dr. Keipes for their support and the IBBL (Integrated Biobank of Luxembourg) for the overall setup of the sample collection, processing, and provision. We thank Komal Baig for the setup of the meta-analysis. We thank Tony Kaoma and Dr. Petr Nazarov from the LIH bioinformatics platform and Dr. Daniel Perez-Hernandez for the fruitful discussions on the statistical analysis.
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