Blood Protein - Methods summary

Summary

The Blood Proteins section 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. We also present an annotation of the proteins secreted from human cells and tissues (“the secretome”) to predict which genes encode proteins that are actively secreted to blood.

Key publication

Uhlén M et al. (2019) “The human secretome” Sci Signal. 12 (609): aaz0274 and Uhlen M et al. (2019) “A genome-wide transcriptomic analysis of protein-coding genes in human blood cells” Science 366 (6472): aax9198

What can you learn from the Blood Proteins section?

Learn about

• concentration of human plasma proteins based on immune assays and MS
• expression of plasma proteins in healthy individuals based on PEA
• classification of the human secreted proteins

How has the data been generated?

The plasma proteome levels from healthy individuals were measured using proximity extension assay (PEA). The healthy individuals were followed longitudinal for two years and the plasma proteome levels were measured every three months. Data generated by proximity extension assays was normalized within and between plates followed by transformation using a predetermined correction factor and provided in the arbitrary unit Normalized Protein eXpression (NPX). 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. The Blood proteins section also contains an annotation of the human secretome classified into different categories, including secreted to blood, secreted locally and matrix proteins.

How was the classification of the human secretome done?

The potentially secreted proteins, identified as proteins with a signal peptide and no transmembrane-spanning region, were systematically analysed using literature, bioinformatics and experimental data to predict and annotate their final location in the human body, in particular if active secretion into blood could be expected. Each gene was annotated with a single location and the categories and their hierarchy is displayed in the figure. A large portion of the proteins was annotated as intracellular, including locations in the Golgi, ER and other intracellular compartments.

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 gender.

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.