PXD044053

PXD044053 is an original dataset announced via ProteomeXchange.

Title	A multi-center collaborative study to optimize mass spectrometry workflows of clinical specimen
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.
HostingRepository	PRIDE
AnnounceDate	2024-01-05
AnnouncementXML	Submission_2024-01-04_21:22:04.462.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christine von Toerne
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; timsTOF

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-24 19:16:02	ID requested
⏵ 1	2024-01-04 21:22:05	announced

Kardell O, von Toerne C, Merl-Pham J, K, ö, nig AC, Blindert M, Barth TK, Mergner J, Ludwig C, T, ü, shaus J, Eckert S, M, ü, ller SA, Breimann S, Giesbertz P, Bernhardt AM, Schweizer L, Albrecht V, Teupser D, Imhof A, Kuster B, Lichtenthaler SF, Mann M, Cox J, Hauck SM, Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens. J Proteome Res, 23(1):117-129(2024) [pubmed]

10.1021/acs.jproteome.3c00473;

submitter keyword: Round robin study, DIA, LC-MS, mass spectrometry, clinical specimen, Plasma, CSF, intra-laboratory, DDA, inter-laboratory

Stefanie M. Hauck
contact affiliation	Metabolomics and Proteomics Core (MPC), Helmholtz Zentrum München GmbH German Research Center for Environmental Health, Munich, Germany
contact email	Stefanie.Hauck@helmholtz-munich.de
lab head
Christine von Toerne
contact affiliation	Helmholtz Zentrum München
contact email	vontoerne@helmholtz-muenchen.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/01/PXD044053

PRIDE project URI

• PRIDE
  1. PXD044053
     1. Label: PRIDE project
     2. Name: A multi-center collaborative study to optimize mass spectrometry workflows of clinical specimen