Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis
Metabolomic and proteomic analyses of human plasma and serum samples harbor the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, pr...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.961448/full |
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| author | Hagen M. Gegner Thomas Naake Aurélien Dugourd Torsten Müller Torsten Müller Felix Czernilofsky Georg Kliewer Georg Kliewer Evelyn Jäger Barbara Helm Nina Kunze-Rohrbach Ursula Klingmüller Carsten Hopf Carsten Müller-Tidow Sascha Dietrich Julio Saez-Rodriguez Wolfgang Huber Rüdiger Hell Gernot Poschet Jeroen Krijgsveld Jeroen Krijgsveld |
| author_facet | Hagen M. Gegner Thomas Naake Aurélien Dugourd Torsten Müller Torsten Müller Felix Czernilofsky Georg Kliewer Georg Kliewer Evelyn Jäger Barbara Helm Nina Kunze-Rohrbach Ursula Klingmüller Carsten Hopf Carsten Müller-Tidow Sascha Dietrich Julio Saez-Rodriguez Wolfgang Huber Rüdiger Hell Gernot Poschet Jeroen Krijgsveld Jeroen Krijgsveld |
| author_sort | Hagen M. Gegner |
| collection | DOAJ |
| description | Metabolomic and proteomic analyses of human plasma and serum samples harbor the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implementing a unified proteomic and metabolomic approach in a clinical setting, we assessed the influence of temperature, sitting times, and centrifugation speed on the plasma and serum metabolomes and proteomes from six healthy volunteers. We used targeted metabolic profiling (497 metabolites) and data-independent acquisition (DIA) proteomics (572 proteins) on the same samples generated with well-defined pre-analytical conditions to evaluate criteria for pre-analytical SOPs for plasma and serum samples. Time and temperature showed the strongest influence on the integrity of plasma and serum proteome and metabolome. While rapid handling and low temperatures (4°C) are imperative for metabolic profiling, the analyzed proteomics data set showed variability when exposed to temperatures of 4°C for more than 2 h, highlighting the need for compromises in a combined analysis. We formalized a quality control scoring system to objectively rate sample stability and tested this score using external data sets from other pre-analytical studies. Stringent and harmonized standard operating procedures (SOPs) are required for pre-analytical sample handling when combining proteomics and metabolomics of clinical samples to yield robust and interpretable data on a longitudinal scale and across different clinics. To ensure an adequate level of practicability in a clinical routine for metabolomics and proteomics studies, we suggest keeping blood samples up to 2 h on ice (4°C) prior to snap-freezing as a compromise between stability and operability. Finally, we provide the methodology as an open-source R package allowing the systematic scoring of proteomics and metabolomics data sets to assess the stability of plasma and serum samples. |
| first_indexed | 2024-04-12T00:45:41Z |
| format | Article |
| id | doaj.art-13786df52f9646db9487239e968656a6 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-12T00:45:41Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-13786df52f9646db9487239e968656a62022-12-22T03:54:53ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-12-01910.3389/fmolb.2022.961448961448Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysisHagen M. Gegner0Thomas Naake1Aurélien Dugourd2Torsten Müller3Torsten Müller4Felix Czernilofsky5Georg Kliewer6Georg Kliewer7Evelyn Jäger8Barbara Helm9Nina Kunze-Rohrbach10Ursula Klingmüller11Carsten Hopf12Carsten Müller-Tidow13Sascha Dietrich14Julio Saez-Rodriguez15Wolfgang Huber16Rüdiger Hell17Gernot Poschet18Jeroen Krijgsveld19Jeroen Krijgsveld20Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, GermanyGenome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyBioquant, Faculty of Medicine, Institute for Computational Biomedicine, University of Heidelberg and Heidelberg University Hospital, Heidelberg, GermanyFaculty of Medicine, University of Heidelberg, Heidelberg, GermanyDivision Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, GermanyDepartment of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, GermanyFaculty of Medicine, University of Heidelberg, Heidelberg, GermanyDivision Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, GermanyCenter for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, GermanyDivision Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, GermanyCentre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, GermanyDivision Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, GermanyCenter for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, GermanyDepartment of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, GermanyDepartment of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, GermanyBioquant, Faculty of Medicine, Institute for Computational Biomedicine, University of Heidelberg and Heidelberg University Hospital, Heidelberg, GermanyGenome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, GermanyCentre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, GermanyCentre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, GermanyFaculty of Medicine, University of Heidelberg, Heidelberg, GermanyDivision Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, GermanyMetabolomic and proteomic analyses of human plasma and serum samples harbor the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implementing a unified proteomic and metabolomic approach in a clinical setting, we assessed the influence of temperature, sitting times, and centrifugation speed on the plasma and serum metabolomes and proteomes from six healthy volunteers. We used targeted metabolic profiling (497 metabolites) and data-independent acquisition (DIA) proteomics (572 proteins) on the same samples generated with well-defined pre-analytical conditions to evaluate criteria for pre-analytical SOPs for plasma and serum samples. Time and temperature showed the strongest influence on the integrity of plasma and serum proteome and metabolome. While rapid handling and low temperatures (4°C) are imperative for metabolic profiling, the analyzed proteomics data set showed variability when exposed to temperatures of 4°C for more than 2 h, highlighting the need for compromises in a combined analysis. We formalized a quality control scoring system to objectively rate sample stability and tested this score using external data sets from other pre-analytical studies. Stringent and harmonized standard operating procedures (SOPs) are required for pre-analytical sample handling when combining proteomics and metabolomics of clinical samples to yield robust and interpretable data on a longitudinal scale and across different clinics. To ensure an adequate level of practicability in a clinical routine for metabolomics and proteomics studies, we suggest keeping blood samples up to 2 h on ice (4°C) prior to snap-freezing as a compromise between stability and operability. Finally, we provide the methodology as an open-source R package allowing the systematic scoring of proteomics and metabolomics data sets to assess the stability of plasma and serum samples.https://www.frontiersin.org/articles/10.3389/fmolb.2022.961448/fullproteomicsmetabolomicsplasmasample preparationbiomarker |
| spellingShingle | Hagen M. Gegner Thomas Naake Aurélien Dugourd Torsten Müller Torsten Müller Felix Czernilofsky Georg Kliewer Georg Kliewer Evelyn Jäger Barbara Helm Nina Kunze-Rohrbach Ursula Klingmüller Carsten Hopf Carsten Müller-Tidow Sascha Dietrich Julio Saez-Rodriguez Wolfgang Huber Rüdiger Hell Gernot Poschet Jeroen Krijgsveld Jeroen Krijgsveld Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis Frontiers in Molecular Biosciences proteomics metabolomics plasma sample preparation biomarker |
| title | Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis |
| title_full | Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis |
| title_fullStr | Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis |
| title_full_unstemmed | Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis |
| title_short | Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis |
| title_sort | pre analytical processing of plasma and serum samples for combined proteome and metabolome analysis |
| topic | proteomics metabolomics plasma sample preparation biomarker |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.961448/full |
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