An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics

Knecht, Sascha; Eberl, H. Christian; Kreisz, Norbert; Ugwu, Ukamaka Juliet; Starikova, Tatiana; Kuster, Bernhard; Wilhelm, Stephanie

doi:10.1016/j.mcpro.2023.100636

“…Sample collection and processing methods, including sample storage conditions and protein extraction protocols, may also impact the reproducibility and reliability of proteomic data [147,148]. Moreover, the complexity of the bone proteome, including the presence of low-abundance proteins and PTMs, poses analytical challenges for protein identification and quantification [149,150]. Additionally, standardization of proteomic workflows, data analysis pipelines, and quality control (QC) measures is essential to ensure the robustness and reproducibility of proteomic studies in osteoporosis research [151,152].…”

Section: Limitations and Challenges In Proteomic Studies Of Osteoporosismentioning

confidence: 99%

Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers and Therapeutic Targets for the Metabolic Bone Disease

Wang,

Xue,

Hu

et al. 2024

Preprint

3

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Osteoporosis (OP), a prevalent skeletal disorder characterized by compromised bone strength and increased susceptibility to fractures, poses a significant public health concern. This review aims to provide a comprehensive analysis of the current state of research in the field, focusing on the application of proteomic techniques to elucidate diagnostic markers and therapeutic targets for OP. The integration of cutting-edge proteomic technologies has enabled the identification and quantification of proteins associated with bone metabolism, leading to a deeper understanding of the molecular mechanisms underlying OP. In this review, we systematically examine recent advancements in proteomic studies related to OP, emphasizing the identification of potential biomarkers for OP diagnosis and the discovery of novel therapeutic targets. Additionally, we discuss the challenges and future directions in the field, highlighting the potential impact of proteomic research in transforming the landscape of OP diagnosis and treatment.

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“…Sample collection and processing methods, including sample storage conditions and protein extraction protocols, may also impact the reproducibility and reliability of proteomic data [152,153]. Moreover, the complexity of the bone proteome, including the presence of low-abundance proteins and PTMs, poses analytical challenges for protein identification and quantification [154,155]. Additionally, the standardization of proteomic workflows, data analysis pipelines, and quality control (QC) measures is essential to ensure the robustness and reproducibility of proteomic studies in osteoporosis research [156,157].…”

Section: Limitations and Challenges In Proteomic Studies Of Osteoporosismentioning

confidence: 99%

Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers of and Therapeutic Targets for the Metabolic Bone Disease

Wang,

Xue,

Hu

et al. 2024

Biomolecules

1

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Osteoporosis (OP), a prevalent skeletal disorder characterized by compromised bone strength and increased susceptibility to fractures, poses a significant public health concern. This review aims to provide a comprehensive analysis of the current state of research in the field, focusing on the application of proteomic techniques to elucidate diagnostic markers and therapeutic targets for OP. The integration of cutting-edge proteomic technologies has enabled the identification and quantification of proteins associated with bone metabolism, leading to a deeper understanding of the molecular mechanisms underlying OP. In this review, we systematically examine recent advancements in proteomic studies related to OP, emphasizing the identification of potential biomarkers for OP diagnosis and the discovery of novel therapeutic targets. Additionally, we discuss the challenges and future directions in the field, highlighting the potential impact of proteomic research in transforming the landscape of OP diagnosis and treatment.

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“…MS-based proteomic analysis is notoriously challenging in serum-supplemented cell-culture conditions due to the highly dynamic range of serum proteins 33 . In standard cell-culture conditions, fetal bovine serum (FBS) introduces a high concentration of exogenous proteins that hinder the detection of endogenously secreted proteins from cultured cells at lower levels.…”

Section: Identification Of the Monocyte Sasp In Standard Culture Cond...mentioning

confidence: 99%

A plasma proteomic signature links secretome of senescent monocytes to aging- and obesity-related clinical outcomes in humans

Olinger,

Banarjee,

Dey

et al. 2024

Preprint

0

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Cellular senescence increases with age and contributes to age-related declines and pathologies. We identified circulating biomarkers of senescence associated with diverse clinical traits in humans to facilitate future non-invasive assessment of individual senescence burden and efficacy testing of novel senotherapeutics. Using a novel nanoparticle-based proteomic workflow, we profiled the senescence-associated secretory phenotype (SASP) in monocytes and examined these proteins in plasma samples (N = 1060) from the Baltimore Longitudinal Study of Aging (BLSA). Machine learning models trained on monocyte SASP associated with several age-related phenotypes in a test cohort, including body fat composition, blood lipids, inflammation, and mobility-related traits, among others. Notably, a subset of SASP-based predictions, including a ‘high impact’ SASP panel that predicts age- and obesity-related clinical traits, were validated in InCHIANTI, an independent aging cohort. These results demonstrate the clinical relevance of the circulating SASP and identify relevant biomarkers of senescence that could inform future clinical studies.

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An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics

Cited by 12 publications

References 139 publications

Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers and Therapeutic Targets for the Metabolic Bone Disease

Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers and Therapeutic Targets for the Metabolic Bone Disease

Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers of and Therapeutic Targets for the Metabolic Bone Disease

A plasma proteomic signature links secretome of senescent monocytes to aging- and obesity-related clinical outcomes in humans

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