TY  - JOUR
AU  - Kardell, Oliver
AU  - von Toerne, Christine
AU  - Merl-Pham, Juliane
AU  - König, Ann-Christine
AU  - Blindert, Marcel
AU  - Barth, Teresa K
AU  - Mergner, Julia
AU  - Ludwig, Christina
AU  - Tüshaus, Johanna
AU  - Eckert, Stephan
AU  - Müller, Stephan A
AU  - Breimann, Stephan
AU  - Giesbertz, Pieter
AU  - Bernhardt, Alexander Maximilian
AU  - Schweizer, Lisa
AU  - Albrecht, Vincent
AU  - Teupser, Daniel
AU  - Imhof, Axel
AU  - Kuster, Bernhard
AU  - Lichtenthaler, Stefan F
AU  - Mann, Matthias
AU  - Cox, Jürgen
AU  - Hauck, Stefanie M
TI  - Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens.
JO  - Journal of proteome research
VL  - 23
IS  - 1
SN  - 1535-3893
CY  - Washington, DC
PB  - ACS Publications
M1  - DZNE-2024-00042
SP  - 117 - 129
PY  - 2024
AB  - The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the 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 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. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.
KW  - Tandem Mass Spectrometry: methods
KW  - Chromatography, Liquid: methods
KW  - Workflow
KW  - Reproducibility of Results
KW  - Plasma: chemistry
KW  - LC–MS (Other)
KW  - LC–MS (Other)
KW  - LC–MS (Other)
KW  - CSF (Other)
KW  - LC–MS (Other)
KW  - R package mpwR (Other)
KW  - clinical specimen (Other)
KW  - data-dependent acquisition (Other)
KW  - data-independent acquisition (Other)
KW  - interlaboratory (Other)
KW  - intralaboratory (Other)
KW  - mass spectrometry (Other)
KW  - plasma (Other)
KW  - round-robin study (Other)
LB  - PUB:(DE-HGF)16
C2  - pmc:PMC10775142
C6  - pmid:38015820
DO  - DOI:10.1021/acs.jproteome.3c00473
UR  - https://pub.dzne.de/record/266784
ER  -