Evaluating the effects of preanalytical variables on the stability of the human plasma proteome
Section snippets
Biospecimen Research Network specimens
Donors gave consent for blood collection for research purposes as part of a UCSF Institutional Review Board-approved protocol. Male and female donors (aged 20–40, median 27, Supplemental Table 1) were requested to fast for a minimum of 12 h prior to blood collection. Donors were seated at least 5 min before the draw and the arm was positioned on a slanting armrest in a straight line from the shoulder to the wrist. A tourniquet was applied approximately 2 inches above the antecubital fossa or
Results
We evaluated the effects of several preanalytical variables related to handling, processing, and storage on the stability of plasma and serum proteomes. To this end, we examined the following variables: time and temperature from specimen collection to processing, plasma centrifugation method, number of freeze–thaw cycles, and time in storage at −80 °C. Effort was made to closely control, during blood collection, all parameters known to impinge on specimens’ properties, i.e., variations in the
Discussion
We conducted a systematic analysis to determine the relationships among blood processing and storage variables and the quality and reproducibility of quantitative proteomics data. Multiple processing and storage variables were assayed: (1) time and temperature before processing; (2) time after thawing prior to immunodepletion; (3) centrifugation steps (single vs double); (4) number of freeze–thaw cycles; and (5) time in frozen storage. An untargeted comparative proteomics approach applied to
Acknowledgments
This project has been funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E (UCSF) and PPG Grants P01HD30367, UL1RR024153, and UL1TR000005 (University of Pittsburgh Clinical and Translational Science Institute). The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or
References (47)
- et al.
The human plasma proteome: history, character, and diagnostic prospects
Mol. Cell. Proteomics
(2002) - et al.
The dynamic range problem in the analysis of the plasma proteome
J. Proteomics
(2010) - et al.
Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)
Mol. Cell. Proteomics
(2013) How to improve reliability and efficiency of research about molecular markers: roles of phases, guidelines, and study design
J. Clin. Epidemiol.
(2007)- et al.
Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma
Mol. Cell. Proteomics
(2014) - et al.
Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry
Mol. Cell. Proteomics
(2006) Binding of human interferons to immobilized albumin
Methods Enzymol.
(1981)- et al.
Streptococcal protein G. Gene structure and protein binding properties
J. Biol. Chem.
(1991) - et al.
Structure of serum albumin
Adv. Protein Chem.
(1994) Serum albumin
Adv. Protein Chem.
(1985)
Identification of evidence-based biospecimen quality-control tools: a report of the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group
J. Mol. Diagn.
Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label-free quantitative data-independent LC-MS
Proteomics
Cancer biomarker discovery: opportunities and pitfalls in analytical methods
Electrophoresis
Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies
J. Proteome Res.
Biospecimen reporting for improved study quality
Biopreserv. Biobank.
HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples
Proteomics
Analysis of the molecular quality of human tissues: an experience from the Cooperative Human Tissue Network
Am. J. Clin. Pathol.
Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group
J. Proteome Res.
Inhibition of intrinsic proteolytic activities moderates preanalytical variability and instability of human plasma
J. Proteome Res.
Global stability of plasma proteomes for mass spectrometry-based analyses
Mol. Cell. Proteomics
Evaluation of blood collection tubes using selected reaction monitoring MS: implications for proteomic biomarker studies
Proteomics
The effect of pre-analytical variability on the measurement of MRM-MS-based mid- to high-abundance plasma protein biomarkers and a panel of cytokines
PLoS One
Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction
J. Proteome Res.
Cited by (42)
Proteins in the pathway from high red blood cell width distribution to all-cause mortality
2022, eBioMedicineCitation Excerpt :In accordance with the guidelines for protein biomarker work, all samples were stored at 4 °C, centrifuged for 4 h, immediately aliquoted, and frozen at −80 °C.7 Plasma proteins remain stable for 14–17 years in storage at −80 °C and for up to 25 freeze–thaw cycles.8,9 The present study measured plasma proteomics at baseline and the 9-year follow-up using the 1·3k HTS SOMAscan assay (SomaLogic, Boulder, CO).10,11
Longitudinal Analysis of Circulating Markers of Bone Turnover Across Multiple Decades in Osteoporotic Women
2022, Journal of Hand SurgeryCitation Excerpt :Each biomarker exhibits different degrees of stability both in vivo and in vitro, and analysis of frozen serum creates the potential for some sample degradation over time. Nonetheless, as reported by Hassis et al,16 human plasma proteins are stable for multiple decades in frozen storage, and the main risk to sample integrity is prolonged time to processing and repeated freeze–thaw cycles. The samples in this study were procured, processed, and archived under stringent Department of Defense protocols and not subject to repeated freeze–thaw cycles.
Effects of differences in pre-analytical processing on blood protein profiles determined with SWATH-MS
2020, Journal of Proteomics