Dataset Information

Prm-PASEF and g-dia-PASEF analysis of plasma samples from colorectal cancer and control patients

ABSTRACT: Quantitative analysis of 10 CRC vs 10 control human plasma samples with the prm-PASEF and g-dia-PASEF acquisition methodes

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: antoine lesur

LAB HEAD: Gunnar Dittmar

PROVIDER: PXD036594 | Pride | 2023-04-11

REPOSITORIES: pride

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Publications

Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics.

Lesur Antoine A Bernardin François F Koncina Eric E Letellier Elisabeth E Kruppa Gary G Schmit Pierre-Olivier PO Dittmar Gunnar G

Journal of proteome research 20230403 6

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 ...[more]

PMID: 37011904

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Project description:A quadrupole time-of-flight mass spectrometry coupled with a trapped ion mobility mass spectrometer operated in parallel accumulation-serial fragmentation mode has recently emerged as proteome profiling platform capable of providing four dimensional features of elution time, collision cross section, precursor and fragment ion masses of peptides. The PASEF mode has demonstrated its superior performance by providing nearly 100% ion sampling efficiency both in data-dependent acquisition and data-independent acquisition modes without sacrificing sensitivity. In addition, the substantial gain in selectivity has been proven in targeted measurements using PASEF integrated parallel reaction monitoring mode. However, because these are emerging technologies in the field of proteomics, their applicability to clinical samples has been less investigated. Cerebrospinal fluid is in direct contact with brain and has been shown to contain biomarkers related to a variety of neurological diseases although the proteomics data have been mainly generated using orbitrap-based mass spectrometers. Thus, we acquired in-depth proteome profiles of human CSF in DDA mode to generate a spectral library of 3,478 proteins. The benefit of applying the spectral library to PRM experiments was demonstrated by using CSF samples from 15 Alzheimer’s disease patients and 19 controls and utilizing the spectral library to determine elution times and ion mobility values of targeting peptide. Further, we acquired DIA data from the same CSF samples, and analyzed using the spectral library without additional efforts to generate study-specific library, which also resulted in sensitive protein identification compared to a library-free approach. Overall, we established resource of CSF proteome profiles with 4D features and demonstrated the significant gain for designing and analyzing targeted and DIA studies, which is expected to facilitate 4D proteomics of CSF to study various neurological disorders.

			Action	DRS
	dia.zip	Other
	exported_area_ratio_and_dotproduct.xlsx	Xlsx
	prm.zip	Other
	skyline.zip	Other