Blood Protein - Methods summarySummaryThe Blood Proteins resource contains information regarding the proteins present in blood. Externally and “In-house” generated data are integrated to explore human plasma protein profiles in healthy individuals. Plasma levels in blood are presented, based both on antibody-based immune assays and mass spectrometry-based proteomics. Key publicationsUhlén M et al. (2019) “The human secretome” Sci signal What can you learn from the Blood Protein section?Learn about
Data overview
How has the data been generated?Plasma proteins were measured with the proximity extension assay (Olink Explore HT, 5,416 protein targets) in two longitudinal cohorts of healthy individuals:
All samples were EDTA plasma. Data were normalized by the provider and reported as Normalized Protein eXpression (NPX), a relative unit on a log2 scale. Values flagged with QC warnings were excluded, as were samples with more than 50% QC warnings. APOE and the proteins in dilution block 8 (n = 68, the most abundant proteins) were excluded for technical reasons. The Blood Atlas also contain information of proteins detected by mass spectrometry-based proteomics, based on publicly available data on the Peptide Atlas. The mass-spectrometry based data was filtered to include only the minimal, non-redundant list of proteins derived from the set of identified peptides and exclude entries labelled as contaminants. In addition, the concentration of actively secreted proteins was annotated using publicly available literature.
Mixed-effects modelsFor each protein and cohort, a linear mixed-effects model was fitted with age and sex as fixed effects and a random intercept per individual. Proteins with more than 80% of samples below the limit of detection (LOD) in a cohort were excluded from that cohort’s analysis. The proportion of variance explained by age and sex (marginal R²), and by the individual (conditional R² minus marginal R²), was estimated with Nakagawa’s R². For proteins with a singular fit, the variance attributed to the individual was set to zero. P-values for the age and sex effects were adjusted with the Benjamini–Hochberg method, and effects with an adjusted p < 0.05 were considered significant. What is presented in the section?In the gene summary page of the Blood Proteins section, the protein levels from the PEA based assays are shown. The longitudinal variation in the expression of a protein in plasma from healthy individuals is displayed in two line plots separated according to sex.
In addition, the gene summary page include the blood concentrations from mass spectrometry studies when available in the Peptide Atlas. The predicted concentration in blood (plasma or serum) is shown.
Furthermore, the blood concentration for the proteins annotated to be secreted to blood is shown (when available). The reported concentration in blood are shown for some representative studies with reference to the literature.
Data tablesDetailed tables for plasma concentrations meansured by differetn techniques. Immunoassay-based plasma concentrationsTable 1. Concentrations for proteins secreted to blood. Measured by immunoassays.
Mass spectrometry-based plasma concentrationsTable 2. A list of the proteins detected in blood by mass spectrometry.
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||