Advances in human proteomics at high scale with the SOMAscan proteomics platform

Tie2 protects the vasculature against thrombus formation in systemic inflammation

“…EDTA-plasma from 7 patients with sepsis and seven patients with sepsis DIC were analyzed using DNA-aptamer-based recognition on the SOMAScan platform (SomaLogic) at the BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center. Samples were prepared and run using the SOMAScan Assay Kit for human plasma, 1.3k (catalog 900-00011), according to the standard protocols from SomaLogic, as described previously (73). Five pooled plasma controls and 1 no-protein buffer control were run in parallel with the samples.…”

Proteomic methods for biomarker discovery and validation. Are we there yet?

“…Historically, effort to discover novel biomarkers in body fluids, especially in plasma or serum, have been challenging owing to the large dynamic range of the proteome and the moderate resolving power of early instruments [5]. But with development of fractionation methods coupled with high precision and high resolution mass spectrometers [6] and advances in affinity array assays [7,8], measuring biomarkers in complex samples is becoming a relatively routine task and has attracted several investigators and biopharmaceutical companies into a race for biomarker discovery and validation.…”

“…In the past 5 years, two useful approaches have matured. Affinity-based protein profiling using antibody bead arrays totaling 4608 antibodies that target 3450 genes [1] and SomaScan technology that uses modified aptamers or SOMAmers targeting 1129 proteins in a single run [8]. Both methods were found to be highly sensitive, requiring only small volume of serum or plasma, with no need for albumin depletion and capable of measuring multiple targets over a wide dynamic range.…”

Sensitivity and specificity: twin goals of proteomics assays. Can they be combined?

“…These alternatives include peptide aptamers isolated by phage and ribosomal display technologies [69], but DNA aptamers stand out as the simplest and most economic to produce. One reason why Gold et al have succeeded in developing the highly multiplexed assays described above is that their SOMAmers have amino acid-like functional groups [63,70]. This chemistry was developed by Eaton et al [71], and forms part of an approach that is advancing in the direction of hybrid molecules that resemble peptides that are compatible with enzymatic amplification [72].…”