Dataset Information

Multi-center longitudinal quality assessment of MS-based proteomics in plasma and serum

ABSTRACT: Advancing MS-based proteomics towards clinical applications evolves around developing standardized start-to-finish and fit-for-purpose workflows for clinical specimens. Steps along the method design involve the determination and optimization of several bioanalytical parameters such as selectivity, sensitivity, accuracy, and precision. In a joint effort eight proteomics laboratories belonging to the MSCoreSys initiative including the CLINSPECT-M, MSTARS, DIASym, and SMART-CARE consortia performed a longitudinal round robin study to assess analysis performance of plasma and serum as clinically relevant samples. A variety of LC-MS/MS setups including mass spectrometer models from ThermoFisher and Bruker, as well as LC systems from ThermoFisher, Evosep, and Waters Corporation were used in this study. As key performance indicators sensitivity, precision and reproducibility were monitored over time. Protein identifications range between 300 to 400 IDs across different state-of-the-art MS instruments, with timsTOF Pro, Orbitrap Exploris 480 and Q Exactive HF-X being among the top performers. Overall, 71 proteins are reproducibly detectable in all setups in both serum and plasma samples and 22 of these proteins are FDA-approved biomarkers, which are reproducibly quantified (CV < 20% with label-free quantification). In total, the round robin study highlights a promising baseline for bringing MS-based measurements of serum and plasma samples closer to clinical utility.

INSTRUMENT(S): Orbitrap Fusion Lumos, timsTOF Pro, Q Exactive HF-X, timsTOF Pro 2, Orbitrap Exploris 480, Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma, Blood Serum

SUBMITTER: Thomas Gronauer

LAB HEAD: Dr. Stefanie Hauck

PROVIDER: PXD054073 | Pride | 2025-02-14

REPOSITORIES: pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	DIA-NN_T1_DIA_A_A_evosep_orbiexp.7z	Other
	DIA-NN_T1_DIA_A_A_ultimate_qexachf.7z	Other
	DIA-NN_T1_DIA_A_B_evosep_orbiexp.7z	Other
	DIA-NN_T1_DIA_A_B_ultimate_qexachf.7z	Other
	DIA-NN_T1_DIA_B_A_ultimate_fuslum.7z	Other

Items per page:

1 - 5 of 1179

Publications

Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum.

Kardell Oliver O Gronauer Thomas T von Toerne Christine C Merl-Pham Juliane J König Ann-Christine AC Barth Teresa K TK Mergner Julia J Ludwig Christina C Tüshaus Johanna J Giesbertz Pieter P Breimann Stephan S Schweizer Lisa L Müller Torsten T Kliewer Georg G Distler Ute U Gomez-Zepeda David D Popp Oliver O Qin Di D Teupser Daniel D Cox Jürgen J Imhof Axel A Küster Bernhard B Lichtenthaler Stefan F SF Krijgsveld Jeroen J Tenzer Stefan S Mertins Philipp P Coscia Fabian F Hauck Stefanie M SM

Journal of proteome research 20250207

Advancing MS-based proteomics toward clinical applications evolves around developing standardized start-to-finish and fit-for-purpose workflows for clinical specimens. Steps along the method design involve the determination and optimization of several bioanalytical parameters such as selectivity, sensitivity, accuracy, and precision. In a joint effort, eight proteomics laboratories belonging to the MSCoreSys initiative including the CLINSPECT-M, MSTARS, DIASyM, and SMART-CARE consortia performed ...[more]

PMID: 39918541

Similar Datasets

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.

Project description:Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations. A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and five growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation. During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the regulation of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant. The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90 % of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects,, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures. This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied. In the study presented here mRNA stabilities were analyzed at 5 growth rates. For each growth rate mRNA levels were measured in a time course experiment following rifampicin addition. At least 12 time points per growth rate are available, including 3 replicates of the zero.

Project description:Alcohol consumption induces hepatocyte damage through complex processes involving oxidative stress and disrupted metabolism. Combined, these factors alter proteomic and epigenetic marks providing a critical opportunity to identify therapeutic targets. Indeed, alcohol-induced protein acetylation is a key post-translational modification (PTM) that regulates hepatic metabolism and is associated with the pathogenesis of alcohol-associated liver disease (ALD). Interestingly, recent evidence suggests lysine acetylation occurs when a proximal cysteine residue is within ~15 Å of a lysine residue, referred to as a cysteine-lysine (Cys-Lys) pair. Here, acetylation can occur through the transfer of an acetyl moiety via an S à N acetyl transfer reaction. Alcohol-mediated hepatic redox stress is known to occur coincident with lysine acetylation, but the biochemical mechanisms related to cysteine and lysine crosstalk within ALD remain unexplored. A chronic murine model of ALD was employed to quantify hepatic cysteine redox and lysine acetylation, revealing that alcohol metabolism significantly reduced the cysteine proteome and increased protein acetylation. Interrogating both cysteine redox and lysine acetylation datasets, 1,281 proteins were mapped by AlphaFold2 to quantify distances between 557,815 cysteine and lysine residues. This process identified 388,698 Cys-Lys pairs that were further used to evaluate thiol redox signaling. Our analysis reveals that alcohol metabolism induces redox changes and acetylation selectively on proximal Cys-Lys pairs with an odds ratio of 1.89 (p< 0.0001). We also identified key redox signaling hubs embedded in metabolic pathways associated with ALD, including lipid metabolism, the TCA cycle, and the electron transport chain. Specific protein targets embedded across these pathways include Echs1, Glrx5, Decr2, and Adh1, among many others. Interestingly, these proximal Cys-Lys exist as four major protein motifs represented by the number of Cys and Lys residues that are pairing (Cysx-Lysx). These motifs include Cys1:Lys1, Cysx:Lys1, Cys1:Lysx and Cysx:Lysx each with a unique microenvironment likely indicative of the mode of enzymatic regulation occurring. The motifs are composed of functionally relevant amino acids altered within ALD, identifying sites of therapeutic potential. Furthermore, these unique Cys-Lys redox signatures are translationally relevant as revealed by orthologous comparison with severe alcohol-associated hepatitis (SAH) explants, revealing numerous pathogenic thiol redox signals in these patients.

Project description:Acute respiratory distress syndrome (ARDS) carries about a 50 percent mortality and is frequently associated with an infection (sepsis). Life-support treatment with mechanical ventilation rescues many patients, although superimposed infection or multiple organ failure can result in death. The outcome of a patient developing sepsis highly depends on the degree of pre-existing inflammation prior to the infection. In this study, we describe each stage of the inflammation process using a transcriptional approach and an animal model. Femelle C57BL6/J mice received an intraveinous oleic acid injection to induce an acute lung injury. PBMC expression patterns have been analyzed using a 9900 cDNA mouse microarray (MUSV29K). Our gene-expression analysis revealed marked changes in the immune and inflammatory response metabolic pathways, notably lipid metabolism and transcription. The early pro-inflammatory stage (1H-1H30) is characterized by the release of immune response and activation of inflammatory mechanisms. Later (3H-4H), the immune cells migrate into inflamed tissues through interaction with vascular endothelial cells. Finally, at late stages of lung inflammation (18H-24H), metabolism is deeply disturbed. Highly expressed pro-inflammatory cytokines activate transcription of many genes as well as lipid metabolism. This global overview of critical events occuring during lung inflammation is essential to understand infectious pathologies such as sepsis where inflammation and infection are interwined. From now on, it becomes possible to isolate the impact of a pathogen at the transcriptional level from the global gene expression modifications resulting from the infection associated with the inflammation. Also, our work allowed to identify genes involved in the response to inflammation. Among those, several may be potential target for gene therapy. Wild-type femelle C57Bl/6J mice, 7 weeks old, were obtained from Charles River and housed in a specific pathogen-free animal facility. We studied 39 mice divided into 6 groups. Each group was identified according to the incubation time: 1H, 1H30, 3H, 4H, 18H and 24H. The 1H group was made up of 6 mice (2 physiological serum and 4 OA); the 1H30 group was made up of 8 mice (2 physiological serum and 6 OA); the 3H group was made up of 7 mice (2 physiological serum and 5 OA); the 4H group was made up of 6 mice (2 physiological serum and 4 OA); the 18H group was made up of 6 mice (2 physiological serum and 4 OA); the 24H group was made up of 6 mice (2 physiological serum and 4 OA). Several RNA samples have been hybridized on 2 filters consisting in technical replicates. Data normalized by quantile without adjustment on physiological serum linked on Series record.