title: Evaluating the effects of preanalytical variables on the stability of the human plasma proteome.
abstract: High quality clinical biospecimens are vital for biomarker discovery, verification, and validation. Variations in blood processing and handling can affect protein abundances and assay reliability. Using an untargeted LC-MS approach, we systematically measured the impact of preanalytical variables on the plasma proteome. Time prior to processing was the only variable that affected the plasma protein levels. LC-MS quantification showed that preprocessing times <6h had minimal effects on the immunodepleted plasma proteome, but by 4 days significant changes were apparent. Elevated levels of many proteins were observed, suggesting that in addition to proteolytic degradation during the preanalytical phase, changes in protein structure are also important considerations for protocols using antibody depletion. As to processing variables, a comparison of single- vs double-spun plasma showed minimal differences. After processing, the impact ⩽3 freeze-thaw cycles was negligible regardless of whether freshly collected samples were processed in short succession or the cycles occurred during 14-17 years of frozen storage (-80 °C). Thus, clinical workflows that necessitate modest delays in blood processing times or employ different centrifugation steps can yield valuable samples for biomarker discovery and verification studies.
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
authors.forename: Maria E
authors.initials: ME
authors.lastname: Hassis
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Niles
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
authors.forename: Miles N
authors.initials: MN
authors.lastname: Braten
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Albertolle
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
authors.forename: H
authors.initials: H
authors.lastname: Ewa Witkowska
authors.affiliation: Magee-Womens Research Institute and Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Carl A
authors.initials: CA
authors.lastname: Hubel
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Fisher
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA. Electronic address: katherine.williams@ucsf.edu.
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Williams
mesh_terms: D001798:Blood Proteins / Q000032:analysis*; D002498:Centrifugation; D002853:Chromatography, Liquid; D005615:Freezing; D006801:Humans; D055550:Protein Stability; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D013048:Specimen Handling
chemical_list: D001798:Blood Proteins; D020543:Proteome
keywords: Mass spectrometry; Plasma; Preanalytical variables; Proteomics; Serum