Dataset Information

Analysis of 1,508 plasma samples of the DiOGenes study - Robust, single shot capillary flow data-independent acquisition to decipher proteomic profiles of weight loss and maintenance

ABSTRACT: Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies (1, 2), we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined a optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform is capable of measuring 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1,508 samples.

INSTRUMENT(S): TripleTOF 5600, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Roland Bruderer

LAB HEAD: Lukas Reiter

PROVIDER: PXD013231 | Pride | 2019-04-05

REPOSITORIES: Pride

ACCESS DATA

Publications

Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance.

Bruderer Roland R Muntel Jan J Müller Sebastian S Bernhardt Oliver M OM Gandhi Tejas T Cominetti Ornella O Macron Charlotte C Carayol Jérôme J Rinner Oliver O Astrup Arne A Saris Wim H M WHM Hager Jörg J Valsesia Armand A Dayon Loïc L Reiter Lukas L

Molecular & cellular proteomics : MCP 20190404 6

Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limita ...[more]

PMID: 30948622

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Project description:The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is to develop standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight common ground in a diverse landscape of different sample preparation techniques and LC-MS setups with the aim to explore differences and potential confounding factors as well as to identify areas for improvement with a direct practical benefit. With the aim to benchmark and improve current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium we performed two consecutive round robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six participating study partners were provided with two clinically relevant sample matrices: plasma, and cerebrospinal fluid (CSF). In the first round each laboratory applied their current best practice protocol for the respective matrix, covering laboratory-specific sample proteolysis, liquid chromatography, and MS measurement procedure. All resulting MS files were analyzed centrally by a standardized pipeline. Based on the achieved results and following a fully transparent exchange of all lab-specific protocols within the consortium, each laboratory could improve their methods before measuring the same samples in a second acquisition round. The results of both measurement time points are compared with respect to identifications (IDs), data completeness, retention time and quantitative precision as well as inter-laboratory reproducibility. For instance, the number of identified protein groups was increased on average by 14% for CSF and 5% for plasma from first to second measurement round across participants resulting in a median overlap number of 579 protein groups for CSF and 246 IDs for plasma across setups. The individual performances of participating study centers and the inter-laboratory reproducibility were improved in the second measurement, emphasizing the effect and importance of expert-driven exchange of best practices. In total, the study not only clearly demonstrates the beneficial effect of sharing knowledge and expertise for direct practical improvements but also highlights tendencies such as common limits of detection or preferable preparation strategies.

Dataset Information

Analysis of 1,508 plasma samples of the DiOGenes study - Robust, single shot capillary flow data-independent acquisition to decipher proteomic profiles of weight loss and maintenance

Publications

Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance.

Similar Datasets

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