SomaScan® Menu Terminology
View our list of SomaScan® Menu Terminology
Primary SOMAmer® Reagent and Protein Target Annotation
SeqId – The SomaLogic® identifier for this sequence.
SomaId – The SomaLogic identifier for this target protein.
Target Name – The SomaLogic name for this target protein.
Target Full Name – The SomaLogic full name for this target protein.
UniProt ID – The UniProt identifier for this target protein.
Type – The assay type of this SOMAmer reagent, ‘Protein’ indicates a sequence that is expected to bind a protein target.
Organism – The organism in which this SOMAmer reagent’s target protein is expressed.
Dilution – The dilution group of this sequence in the SomaScan® Assay version 4.1.
SELEX Target Accession – The accession used by the protein target supplier to identify the SELEX target, may be from RefSeq, UniProt, European Nucleotide Archive or others.
SELEX Target Amino Acid Range – The amino acid range subset of the protein used to produce the SOMAmer reagent per the referenced accession number if provided by the protein supplier.
Protein Constuct Graph – The primary amino acid sequence of the protein used in the development of each SOMAmer reagent dictates the epitopes available for binding. SOMAmer reagents may be developed against full-length or truncated proteins, different protein domains, isoforms, etc. This graph indicates the primary amino acid sequence of the recombinant protein (grey or blue bar) used in the selection of each reagent (y-axis) relative to the amino acid sequence of the full-length analyte (x-axis, black bar). The SOMAmer reagent binding epitope will be somewhere within the range of the protein construct used to select the reagent.
SELEX Target Expression System – The class of expression system used by the protein supplier to produce the protein target, if provided by the supplier.
Buffer Performance
Apparent Kd (M) – The apparent binding affinity for this SOMAmer reagent and target under SomaScanlike
assay conditions.
LoDB (RFU) – The LoD is defined as the lowest concentration of an analyte that can be consistently detected in a defined type of specimen. The Clinical Laboratory Standards Institute (CLSI) defines the LoD based on results for repeated blank (buffer) samples in conjunction with the lowest concentrations of protein spikes into buffer. Typically, it is computed as
LoD = mean_blank + 1.64 σ_blank + 1.64 σ_low
See CLSI definitions, Armbruster and Pry. Clin Biochem
Rev. 2008 Aug 29 (Suppl 1), S49-S52.
It can be shown from SomaScan Assay titrations that variance for buffer samples is close to the variance for
low protein concentrations, and that replacing σ_low with σ_blank in the LoD computations yields a good approximation. We also use ‘robust’ estimates to avoid outlier influence in low signal measurements, replacing the mean with the median and the standard deviation with median absolute deviation (σ ≈ 1.48 MAD).
The estimated LoD computation is then:
eLoD = median_blank + 4.9 MAD_blank
Human Plasma Performance
Signal-to-Noise Plasma – The expected signal-to-noise ratio for plasma developed from healthy individuals.
Intra-Plate CV Plasma – The within-run coefficient of variation for SOMAmer reagents run in a test of human plasma from healthy individuals.
Inter-Plate CV Plasma – The between-run coefficient of variation for SOMAmer reagents run in a test of human plasma from healthy individuals.
Total CV Plasma – The coefficient of variation for this SOMAmer reagent in a test of human plasma from healthy individuals.
Correlation Plasma – The average run-to-run correlation coefficient for this SOMAmer reagent in a test human plasma from healthy individuals.
F-Statistic Plasma – The F-statistic derived for this SOMAmer reagent in a test of human plasma from healthy individuals.
Lower 95% Normal Plasma (RFU) – The lower 95% for plasma derived from healthy individuals.
Median Normal Plasma (RFU) – The median value on a test of human plasma derived from healthy individuals.
Upper 95% Normal Plasma (RFU) – The upper 95% for plasma derived from healthy individuals.
Human Serum Performance
Signal-to-Noise Serum – The expected signal-tonoise ratio for a test of serum samples derived from healthy individuals.
Intra-Plate CV Serum – The within-run coefficient of variation for SOMAmer reagents run in a test of human serum from healthy individuals.
Inter-Plate CV Serum – The between-run coefficient of variation for SOMAmer reagents run in a test of human serum from healthy individuals.
Total CV Serum – The coefficient of variation for this SOMAmer reagent in a test of human serum from healthy individuals.
Correlation Serum – The average run-to-run correlation coefficient for this SOMAmer reagent in
a test human serum from healthy individuals.
F-Statistic Serum – The F-statistic derived for this SOMAmer reagent in a test of human serum from healthy individuals.
Lower 95% Normal Serum (RFU) – The lower 95% for serum derived from healthy individuals.
Median Normal Serum (RFU) – The median value on a test of human serum derived from healthy individuals.
Upper 95% Normal Serum (RFU) – The upper 95% for serum derived from healthy individuals.
Characterization
Characterization Info – Results of testing SOMAmer reagents against available proteins with >40% amino acid sequence similarity to the selected target protein by internal pull-down SDS-PAGE and affinity binding experiments.
Orthogonal Strategies – PubMed PBIDs to a variety of methods that use SOMAmer reagent-independent techniques to quantify and confirm protein identity and level of expression. Examples include ELISA, Histochemistry, Western Blot, Particle-Based Immunoassay, and more.
MRM-MS Data – PubMed PBIDs to results of Multiple Reaction Monitoring (MRM), mass spectrometry
technique that determines protein content in a single sample after SOMAmer enrichment.
DDA-MS Data – PubMed PBIDs to results of Data Dependent Acquisition (DDA), mass spectrometry
technique to determine protein content after SOMAmer enrichment, for pull down testing in matrix (plasma, urine, serum).
pQTL – PubMed PBIDs. Proteins may be orthogonally confirmed using a variety of genetic strategies (such as cis pQTL associations) that directly link a gene to a protein and a SOMAmer reagent.
Mass Spec Confirmed – A “Yes” indicates that the identity of the SOMAmer Reagent’s target has
been confirmed by mass spectrometry following pulldown assay.
Secondary Annotation
Entrez Gene Name – The Entrez Gene name for the gene encoding this target protein.
Entrez Gene ID – The Entrez Gene identifier for the gene encoding this target protein.
Ensembl Gene ID – The Ensembl Gene ID for the gene encoding this target protein.
HGNC ID – The HGNC ID for the gene encoding this target protein.
SELEX Target Name – The name of the expected target when SELEX is run.
SELEX Uniprot ID – The UniProt ID of the expected target when SELEX is run.
Version Lifting
Serum Scalar v4.1 to v4.0 – The scale factor to be applied to convert normalized v4.1 data to v4.0.
Serum Lin’s CCC – Lin’s Concordance Correlation Coefficient is a measure of how well lifted data
compares to data collected in the target assay version.
Plasma Scalar v4.1 to v4.0 – The scale factor to be applied to convert normalized v4.1 data to v4.0.
Plasma Lin’s CCC – Lin’s Concordance Correlation Coefficient is a measure of how well lifted data
compares to data collected in the target assay version.