Refining Platelet Purification Methods: Enhancing Proteomics for Clinical Applications
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arXiv
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| Main Authors: | , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866916767827230720 |
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| author | Markhus, Vibecke Fritz-Wallace, Katarina Mjaavatten, Olav Kristoffersen, Einar K. Goplen, Dorota Selheim, Frode |
| author_facet | Markhus, Vibecke Fritz-Wallace, Katarina Mjaavatten, Olav Kristoffersen, Einar K. Goplen, Dorota Selheim, Frode |
| contents | Background: Platelet proteomics offers valuable insights for clinical research, yet isolating high-purity platelets remains a challenge. Current methods often lead to contamination or platelet loss, compromising data quality and reproducibility.
Objectives: This study aimed to optimize a platelet isolation technique that yields high-purity samples with minimal loss and to identify the most effective mass spectrometry-based proteomic method for analyzing platelet proteins with optimal coverage and sensitivity.
Methods: We refined an isolation protocol by adjusting centrifugation time to reduce blood volume requirements while preserving platelet yield and purity. Using this optimized method, we evaluated three proteomic approaches: Label-free Quantification with Data-Independent Acquisition (LFQ-DIA), Label-free Quantification with Data-Dependent Acquisition (LFQ-DDA), and Tandem Mass Tag labeling with DDA (TMT-DDA).
Results: LFQ-DIA demonstrated superior protein coverage and sensitivity compared to LFQ-DDA and TMT-DDA. The refined isolation protocol effectively minimized contamination and platelet loss. Additionally, age-related differences in platelet protein composition were observed, highlighting the importance of using age-matched controls in biomarker discovery studies.
Conclusions: The optimized platelet isolation protocol provides a cost-effective and reliable method for preparing high-purity samples for proteomics. LFQ-DIA is the most suitable approach for comprehensive platelet protein analysis. Age-related variation in platelet proteomes underscores the need for demographic matching in clinical proteomic research. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_24394 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Refining Platelet Purification Methods: Enhancing Proteomics for Clinical Applications Markhus, Vibecke Fritz-Wallace, Katarina Mjaavatten, Olav Kristoffersen, Einar K. Goplen, Dorota Selheim, Frode Biomolecules Genomics Background: Platelet proteomics offers valuable insights for clinical research, yet isolating high-purity platelets remains a challenge. Current methods often lead to contamination or platelet loss, compromising data quality and reproducibility. Objectives: This study aimed to optimize a platelet isolation technique that yields high-purity samples with minimal loss and to identify the most effective mass spectrometry-based proteomic method for analyzing platelet proteins with optimal coverage and sensitivity. Methods: We refined an isolation protocol by adjusting centrifugation time to reduce blood volume requirements while preserving platelet yield and purity. Using this optimized method, we evaluated three proteomic approaches: Label-free Quantification with Data-Independent Acquisition (LFQ-DIA), Label-free Quantification with Data-Dependent Acquisition (LFQ-DDA), and Tandem Mass Tag labeling with DDA (TMT-DDA). Results: LFQ-DIA demonstrated superior protein coverage and sensitivity compared to LFQ-DDA and TMT-DDA. The refined isolation protocol effectively minimized contamination and platelet loss. Additionally, age-related differences in platelet protein composition were observed, highlighting the importance of using age-matched controls in biomarker discovery studies. Conclusions: The optimized platelet isolation protocol provides a cost-effective and reliable method for preparing high-purity samples for proteomics. LFQ-DIA is the most suitable approach for comprehensive platelet protein analysis. Age-related variation in platelet proteomes underscores the need for demographic matching in clinical proteomic research. |
| title | Refining Platelet Purification Methods: Enhancing Proteomics for Clinical Applications |
| topic | Biomolecules Genomics |
| url | https://arxiv.org/abs/2505.24394 |