Gunnar Dittmar, Ph.D. is the group leader of the proteomics of cellular signalling research group at the Luxembourg Institute of Health. After finishing his PhD at the University of Heidelberg, he joined the Lab of Dan Finley at Harvard Medical school as a post-doc. After finishing my Post-Doc, he joined the Max-Delbrück Center for molecular medicine in Berlin as a group leader, starting my own group. At the Delbrück Center, he set up the mass spectrometry core facility, and later he also set up the proteomics core facility at the newly founded Berlin Institute of Health. In 2016 he joined the Luxembourg Institute of Health, where he is still leading the proteomics of cellular signalling group. In parallel, he created the genomic sequencing centre, LuxGen, a joined high throughput sequencing facility and the quantitative biology unit, a technology focused department covering FACS, MRI, Bioinformatics, a reverse protein array and a proteomics platform besides several research groups.
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.
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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. All data were analysed using Skyline. As a less time-consuming alternative to the prm-PASEF method, we describe guided 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.
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