SOMAmer reagents are selected using the SELEX (Systematic Evolution of Ligands using Exponential Enrichment) method, starting with libraries of 1015 molecules and iteratively narrowing that number based on affinity of the rounds of SELEX. Usually about 100 sequences are available after 6 – 8 rounds of SELEX that have acceptable affinity to the target. While all of the SOMAmer reagent candidates will bind the target to varying degrees, the properties of these reagents will vary, including their performance in any given application. While one sequence might perform well in one set of conditions, another sequence may perform better in another. SomaLogic has not tested all SOMAmer reagents in all applications. Please contact technical support at email@example.com or by telephone at 1-800-324-0783 or 303-625-9000 for any questions regarding our reagents.
Do I need to add a carrier to my SOMAmer reagent solution?
Protein carriers, such as bovine serum albumin (BSA), are not necessary for most applications. Addition of detergent, such as 0.001-0.05% Tween-20, will help prevent loss of SOMAmer reagent material to tube walls in very dilute solutions (< 100 pM total DNA). Precise conditions should be determined for each application before use.
What are reasonable storage and handling conditions for SOMAmer reagents? What is known about the stability as a function of temperatures, pH, and buffer conditions?
SOMAmer reagents are stable (e.g., 2 years at -20 °C, 3 months at 4 °C) in solution. SOMAmer reagents should be stored at -20 °C when not in use. They will degrade slowly due to routine sample handling at room temperature, and therefore aliquoting is a highly recommended strategy for long term use to avoid repeated freeze/thaw cycles. Some variation between individual SOMAmer reagents is to be expected. Most typical buffers for biological applications (e.g., HEPES, Tris, PBS) will not adversely affect SOMAmer reagent stability. They are resistant to basic conditions, but will degrade rapidly at pH < 4. The presence of functional groups must also be considered. The standard SOMAmer reagent contains a biotin, which is susceptible to oxidation, especially under unbuffered and/or oxidative conditions.
Do I need to use a competitor in my assay?
Polyanionic competitors can reduce non-specific binding due to the modest affinities some proteins have for random DNA. We recommend using 1 μM SomaLogic Polyanionic Competitor (SomaLogic P/N 910-00001) or 1 mM dextran sulfate as a starting concentration for reducing artifacts for many applications. Higher competitor concentrations can be utilized post-equilibration to selectively enrich for specific binding. Precise conditions should be optimized for each application and SOMAmer reagent. See the Application Note on Polyanionic Competitor use for more details.
Why is a “heat/cool” protocol recommended for SOMAmer reagents?
Some SOMAmer reagent sequences have a tendency to aggregate, or become kinetically trapped in alternative inactive structures, and a heat/cool protocol will restore the correctly folded, monomeric
form. We recommend 5 minutes at 95 °C in a low salt buffer such as 5 mM HEPES, 1 mM EDTA, pH 7.5, followed by cooling to room temperature.
Can I use a SOMAmer reagent as an antagonist?
SOMAmer reagents generally bind conformational epitopes across large contact surface areas, and therefore often inhibit the activities of protein targets by competing with natural binding partners. For this reason, SOMAmer reagents antagonize many functions of their target proteins. If the catalog SOMAmer reagent binds your protein of interest but does not block a function of interest, a custom SOMAmer reagent with these properties may be developed through our SOMAmer Discovery Services business or by obtaining candidate SOMAmer reagents from the original SELEX experiments, called Rapid SOMAmer Candidate Discovery Service. Please contact SomaLogic Technical Support at firstname.lastname@example.org or by telephone at 1-800-324-0783 or 303-625-9000 for more information.
Can SOMAmer reagents be immobilized to solid supports?
SOMAmer reagents are supplied with a biotin moiety on the 5’ end. The biotin will bind to streptavidin coated resins, (i.e. streptavidin, NeutrAvidin, Avidin, CaptAvidin and other streptavidin conjugates) beads, plates and planar surfaces.
Can SOMAmer reagents be used in sandwich assays?
Many SOMAmer reagents have been successfully paired with an antibody for sandwich assays in plate-based (e.g. ELISA) and bead-based (e.g. Luminex) applications. SOMAmer-SOMAmer reagent sandwich pairs have been generated via sandwich SELEX to favor SOMAmer reagent binding to distinct epitopes, and they have also been shown to work in bead-based and plate-based sandwich assays (see Rohloff et al.). If you are interested in developing custom sandwich reagents, please see our application note on that topic and/or contact Technical Support at email@example.com or by telephone at 1-800-324-0783 or 303-625-9000.
Can SOMAmer reagents be used in vivo?
SOMAmer reagents can be used in vivo research purposes but are not intended for use in humans in vivo (i.e. clinical use). SOMAmer reagents are nucleic acids; therefore, they are sensitive to degradation by plasma and tissue nucleases over time. While the chemical modifications on a SOMAmer reagent offer significant resistance to endonuclease degradation, additional modifications are often necessary for in vivo applications. SomaLogic recommends the addition of a 40 kDa PEG to the 5' terminus to prevent renal elimination. In our experience, some SOMAmer reagents do show a partial loss in function upon PEG addition, but the majority do not. However, this modification (or one of similar size) is required for in vivo use in order to increase half-life values from minutes to hours. Phosphodiester backbone protection at nuclease-sensitive sites, including 2'-methoxy and phosphorothioate groups, will provide additional stability. With these modifications, plasma half-life values of 3-6 hours can be achieved in vivo. Cell culture media can contain nucleases, and therefore SOMAmer stability in culture media should be tested empirically.
Please contact SomaLogic Technical Support at firstname.lastname@example.org or by telephone at 1-800- 324-0783 or 303-625-9000 to discuss custom SOMAmer reagent optimization opportunities for optimal SOMAmer reagent performance in your application.
Has this product ever been used for an application that is not listed?
SOMAmer reagents are versatile reagents for use in many affinity-based applications and SOMAmer reagents have been shown to work in most applications that typically use antibodies to bind proteins. SOMAmer reagents have been shown to work in flow cytometry, ELISA-like experiments, sandwich assays with a paired antibody, histochemistry and protein affinity purification applications. Several application notes and references are available here. We encourage users to try SOMAmer reagents in novel applications. We welcome you to share your results and protocols with SomaLogic by contacting us at email@example.com.
How can I confirm SOMAmer reagent concentration?
SOMAmer reagents can be quantified by conjugation of the SOMAmer reagent to a fluorophore (streptavidin phycoerythrin for example), by measuring the absorbance at 260 nm, or by labeling the SOMAmers with a radioactive moiety. SOMAmer reagents are provided with a package insert containing the molar mass of the reagent.
How do I reduce the occurrence of non-specific binding with SOMAmer reagents?
Non-specific binding of SOMAmer reagents may be diminished by adding polyanionic competitors such as herring sperm DNA, yeast tRNA or the SomaLogic Polyanionic Competitor (SomaLogic P/N 910- 00001). After binding, the addition of low molecular weight dextran sulfate can also prevent re-binding of non-specific SOMAmers. Please refer to our application note on use of polyanionic competitors.
How do I release SOMAmer Reagents from solid supports?
Any strategy that releases biotin from streptavidin can be used, but caution is advised in low pH buffers, as SOMAmer reagents degrade rapidly at pH <4.
How do I release SOMAmer reagents from their cognate proteins?
SOMAmer reagents can be released from their targets by denaturation of the protein or denaturation of the SOMAmer reagent. Basic solutions (pH=10 or higher), elevated temperatures or chaotropic salts have successfully been employed.
How stable is the SOMAmer reagent in cell culture?
SOMAmer reagents contain modified nucleotides and a 3’ cap (inverted dT) and are more resistant to both endonuclease and exonuclease degradation than traditional aptamers. Even in as high as 90% human serum, SOMAmer reagents have a nine-fold longer half-life than unmodified DNAs of the same sequence (t 1⁄2 > 48 hours). SomaLogic has found SOMAmer reagents to be functional in cell culture assays for 24- 48 hours.
In which biological matrices will SOMAmer reagents work?
SOMAmer reagents are capable of measuring proteins in a wide array of biological matrices including human serum, plasma, cerebral spinal fluid (CSF), bronchoalveolar lavage (BAL), synovial fluid, nasal lavage, sputum, etc. In addition, many SOMAmer reagents generated to pure human proteins cross- react with non-human orthologues and therefore can be used in SOMAscan to identify differential expression of these analytes in non-human samples. (Please see SomaLogic’s SOMAscan Proteomic Assay Technical White Paper for more information.)
What buffers can I use when working with SOMAmer reagents?
It is recommended to use 40 mM HEPES, 100 mM NaCl, 5 mM KCl, 5 mM MgCl2, 1 mM EDTA, pH 7.5 (total NaCl of approximately 120 mM after pH adjustment with NaOH), as a working buffer. Reagents are likely to perform well in buffers of similar ionic strength and pH, but activity should be tested empirically.
What do I do if the SOMAmer reagent does not work in my application of interest?
While each SOMAmer reagent is tested for affinity to its target, not all SOMAmer reagents have been tested in all applications. Contact technical support at firstname.lastname@example.org or by telephone at 1-800-324-0783 or 303-625-9000 for guidance on how to optimize your protocol for best results.
What is the optimal SOMAmer reagent working concentration?
SOMAmer reagent working concentrations are dependent on the application of interest, but generally range from 10 pM to 1 μM. Please refer to the application notes for guidelines on starting concentrations for various applications.
What kind of functional groups or fluorophores can I put on a SOMAmer reagent?
As synthetic oligonucleotides, SOMAmer reagents can be readily prepared with one or more of numerous functional groups for conjugation to beads or surfaces, as well as for detection in various applications. Our current SOMAmer reagent offering contains a biotin modification. Other typical modifications include an amine, thiol, and/or fluorophores. Custom functionalized SOMAmer reagents are available on request. For more information, please contact SomaLogic Sales at email@example.com or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.
What level of multiplexing can be achieved with SOMAmer reagents?
SomaLogic currently offers commercial measurements of 1,310 unique human proteins in the SOMAscan assay. In proprietary testing, the multiplexing of over 4,000 SOMAmer reagents has been demonstrated with the SOMAscan assay.
Can I get a SOMAmer reagent for a protein not on the list?
Please contact SomaLogic regarding the availability of a reagent to your target of interest or about our SOMAmer Discovery Service. You may complete this form or you may also call us by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.
Can I have the sequence of the SOMAmer reagent that I am using?
The sequence is proprietary to SomaLogic and this information is not disclosed.
Can orders be expedited?
Yes, in most cases we can expedite orders for SOMAmer reagents that are in-stock. Please contact SomaLogic sales at firstname.lastname@example.org or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000 to discuss expedited orders.
Can I submit a bulk order?
SomaLogic will accept bulk orders for SOMAmer reagents and a discount may be available depending on the quantity ordered. Please contact Customer Service at email@example.com or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000 to place a bulk order.
Can SOMAmer reagents be ordered in different amounts?
We offer 500 pmoles of SOMAmer reagent stocks. If you would like to order in bulk amounts, please contact SomaLogic Sales directly at firstname.lastname@example.org or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.
How long does it take to receive my order?
Most SOMAmer reagents are available in-stock at the time of your order, and your order will be processed within 5 business days, depending on quantity. You may expedite the shipping of your order by choosing overnight or the 2-day/Priority shipping option at check-out. Please note however, that international and bulk orders may take longer to process and that overnight delivery is not available to international orders.
How much variability is there between lots of SOMAmer reagents?
As synthetic oligonucleotides, the automated solid phase synthesis process followed by HPLC purification is robust and yields low variability between lots of a given SOMAmer reagent. Typical CVs for purity are 5.0%.
Is there another SOMAmer reagent available for my protein of interest?
Our goal is to provide you with the best reagent for your application. As such, SomaLogic can work with you on a SOMAmer Discovery Service project to deliver multiple SOMAmer reagents from a given SELEX to test in your application. Please contact SomaLogic Sales at email@example.com or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000 for more information.
What do I do if I am missing a tube or my package arrives damaged?
Contact SomaLogic at firstname.lastname@example.org or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000. Please be prepared with your order number, the name of the SOMAmer reagent, and a description of the condition in which the product was received.
What shall I do if the SOMAmer doesn’t work in my application?
While each SOMAmer reagent is tested for affinity to its target, not all SOMAmer reagents have been tested in all applications and as such, SomaLogic cannot guarantee that a SOMAmer Reagent will work in your specific application. Contact Technical Support at email@example.com or by telephone at 1-800-324-0783 or 303-625-9000 for ideas on how to optimize your protocol for best results.
Where can I find copies of documents, protocols, and publications?
Whom do I contact with questions?
Will you discontinue a SOMAmer reagent?
Through our process of continuous quality improvement, SomaLogic works to improve the affinity and specificity of existing SOMAmer reagents. Over time, SomaLogic may replace the currently available SOMAmer reagent for a given target with a new and improved reagent. Please contact SomaLogic Sales to for more information about a custom synthesis of a reagent at firstname.lastname@example.org or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.
Do I need gloves to handle SOMAmer reagents? Are SOMAmer reagents biohazardous? How do I dispose of SOMAmer reagents?
Although SomaLogic has not thoroughly investigated the specific toxicity of each individual SOMAmer reagent, synthetic oligonucleotides are generally considered non-hazardous. SOMAmer reagents do contain functional groups, trace organic salts, and modified nucleic acid bases; therefore, all products should be handled with proper protective equipment (gloves, lab coats, etc.) and universal precautions. Always follow the safety and disposal guidelines for your institution.
Can matrices, high abundance proteins, or other substances interfere with SOMAmer reagent binding?
Binding characteristics of protein-binding reagents, whether SOMAmer reagents or antibodies, will vary depending on the matrix, relative protein concentrations of the target and related proteins, and other factors. Some proteins known to bind to DNA can lead to non-specific binding. Any substance that alters the structure of folded DNA (intercalating dyes for example) could alter the binding properties of SOMAmer reagents. A competitor or blocking reagent may be required, depending on the application.
Can SOMAmer reagents be selected against both non-glycosylated and glycosylated target proteins?
SOMAmer reagents may be selected against non-glycosylated or glycosylated target proteins, and generally binds both forms. However, exceptions may exist, for example if a sugar group sterically blocks the epitope of a SOMAmer reagent selected against a non-glycosylated form, or if glycosylation causes a conformational change in the protein.
Do SOMAmer reagents recognize denatured proteins or linear epitopes?
SOMAmer reagents bind large, conformational epitopes and, therefore, generally do not bind fully denatured target protein or linear epitopes. However, SOMAmer reagents may bind partially denatured target proteins if the epitope retains enough tertiary structure. Please see Jarvis et al. 2015 Structure 23:1-12, Gelinas et al 2014 JBC 289:8720-8734 and Davies et al 2012 PNAS USA 109: 19971-19976 for additional details.
Do SOMAmer reagents recognize post-translational modifications (PTMs)?
SOMAmer reagents typically bind a structure defined by the polypeptide chain. The effect of various PTMs on the binding of a given SOMAmer-protein pair have not been determined for each reagent. SOMAmer reagents that recognize a specific form of a protein with or without a PTM may be identified through our SOMAmer Discovery Service business.
How do I improve specificity in my assay?
Addition of a competitor into a given assay will generally improve specificity. Please refer to the application note on Polyanionic Competitor (P/N 910-00001) use for more details. If you are interested in developing a reagent with unique specificity requirements (e.g. binds one form of a protein and not another or binds all proteins in a given class), please contact SomaLogic at email@example.com or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.
How do you define the purity of a SOMAmer reagent?
The presence of a variety of low level impurities is an inherent challenge in solid phase phosphoramidite synthesis of long oligonucleotides (e.g., N > 50). The highest abundance impurities are slightly shorter versions of the oligonucleotide, missing the 5’ modification, one or more of the 5’ nucleotides, an internal nucleotide, and some combination thereof. Because these molecules differ very slightly from the parent compound, it is difficult to obtain baseline resolution in the chromatographic analysis. In addition, many of these compounds are fully active, and are more correctly thought of as “product-related compounds” and not as impurities or contaminants. It is our philosophy to obtain the highest quality analytical data, and we therefore determine chromatographic purity using a UPLC system and a slow reverse phase gradient, and conservatively cut all partially resolved shoulders when determining the purity value. This typically results in reported purity values in the 50-80% range. This conservative approach allows better evaluation of lot-to-lot consistency. The reported purity may seem low to scientists accustomed to small molecule purity values, which are typically much higher. Therefore, this value should be evaluated together with the functional data (e.g., the binding constant) to properly assess performance of the SOMAmer reagent.
How is SOMAmer reagent specificity determined?
SOMAmer reagents are tested in an affinity capture assay to determine cross reactivity to similar proteins using the SOMAmer target protein as well as closely related proteins (50% or greater identity). Affinity curves are generated for any off-target proteins that demonstrate binding to a SOMAmer reagent in order to determine relative affinities compared to target binding. These results are available on the specification sheets for each reagent.
How is the dissociation constant (Kd) determined in functional testing of a particular protein-SOMAmer interaction?
We perform solution-phase affinity measurements using several methods, depending on the nature of the protein being studied. All measurements are performed with purified protein. In the case of proteins with recombinant tags (i.e. poly-Histidine or Fc) we typically use an AlphaScreen® (Perkin Elmer®) proximity method to detect association of the tagged protein with a biotinylated SOMAmer reagent. In the case of untagged proteins, we typically measure the association of radiolabeled SOMAmer reagent with protein and capture the complex using a non-specific protein-capturing chromatography medium. Saturation binding curves are generated by titrating increasing amounts of protein in the presence of a constant amount of SOMAmer reagent. In the event that the protein-SOMAmer complex cannot be captured, we perform an electrophoretic mobility shift assay (EMSA) in which protein-SOMAmer complexes are detected by a shift in electrophoretic mobility of the radiolabeled SOMAmer reagent on a native gel. The Kd is determined to be the protein concentration at which the half maximal binding is observed. The reported Kd and the Kd measured by the end user may differ based on the assay format, assay conditions, protein source, protein sample purity, or protein modification. Please review the Specification Sheet and Certificate of Analysis for more information on the Kd for a specific SOMAmer reagent.
In what pH range do SOMAmer reagents work?
SOMAmer reagent binding is selected for and tested at pH 7.5. Binding at different pH values should be evaluated for each SOMAmer reagent-protein pair since binding is dependent on proper folding of both the SOMAmer reagent and the protein.
Is it known where the SOMAmer reagent binds the target protein?
Crystal structure analyses of a small number of SOMAmer reagent-protein complexes indicate SOMAmer reagents bind large, conformational epitopes, but the exact epitope of each SOMAmer reagent is not known. Please see Jarvis et al. 2015 Structure 23:1-12, Gelinas et al 2014 JBC 289:8720-8734 and Davies et al 2012 PNAS USA 109: 19971-19976 for additional details.
What are the advantages of SOMAmer reagents over antibodies?
SOMAmer reagents have several distinct advantages over antibodies, including customized in vitro selection conditions, consistent chemical synthesis, superior storage stability, reversible denaturation, and utility in highly multiplexed ligand-binding assays.
What buffers are not compatible with SOMAmer reagents?
Since SOMAmer reagent-protein binding is dependent on proper folding of both the SOMAmer reagent and the protein, denaturing solutions should be avoided. Reducing agents will not affect SOMAmer reagent structure, but are not compatible for proteins containing disulfide bonds. Addition of 1 mM EDTA is acceptable, but higher concentrations should be used with caution since some SOMAmer reagent structures may utilize divalent cations.
Are SOMAmer reagents resistant to nucleases?
SOMAmer reagents are nucleic acids and are sensitive to degradation by endonucleases and exonucleases that recognize DNA substrates. While the chemical groups on a SOMAmer reagent offer significant resistance to endonuclease degradation, additional modifications are often necessary for applications where nucleases may be present. SomaLogic has added an inverted dT to the 3' terminus of the SOMAmer reagents to block exonuclease degradation. Protection against endonucleases is possible via 2'-methoxyribosesor phosphorothioate groups. Please contact SomaLogic Technical Support at firstname.lastname@example.org or by telephone at 1-800-324-0783 or 303-625-9000 to discuss custom SOMAmer reagent optimization opportunities for optimal SOMAmer reagent performance in applications where nuclease stability is required.
Am I permitted to amplify the SOMAmer reagent instead of purchasing more?
No, the sequence is proprietary to SomaLogic and any attempt to determine the sequence is a violation of the license terms that you agreed to upon purchase of the SOMAmer reagent. In the event that we determine that you attempted to reverse engineer the SOMAmer reagent, we reserve the right to no longer provide you SOMAmer reagents.
Can I re-use a SOMAmer reagent?
The answer will vary by application, but in general, SOMAmer reagents can be repeatedly denatured by heat or high pH and re-natured to a fully-active form for re-use.
Am I permitted to sequence a SOMAmer reagent?
No, the sequence is proprietary to SomaLogic and any attempt to determine the sequence is a violation of the license terms that you agreed to upon purchase of the SOMAmer reagent. In the event that we determine that you attempted to reverse engineer the SOMAmer reagent, we reserve the right to no longer provide you SOMAmer reagents.
Do SOMAmer reagents bind their cognate proteins in organic solvents?
SOMAmer reagents are selected to bind their target proteins in an aqueous buffer at pH 7.5 and physiologic ionic strength. In organic solvents, a SOMAmer reagent will likely denature and no longer bind its target protein. However, SOMAmer reagents that have been exposed to organic solvents can be reconstituted in an appropriate aqueous buffer and regain full binding activity after heating to 95°C for 5 minutes and cooling to room temperature, provided the organic solvent did not chemically alter the SOMAmer reagent.
Do SOMAmer reagents run on agarose gels in the same manner as unmodified DNA?
SOMAmer reagents have a phosphodiester backbone and therefore behave much like unmodified DNA or RNA in gel electrophoresis, migrating according to size. The length of a SOMAmer reagent typically ranges from 25-80 nucleotides, and therefore separation can be achieved on 8-20% polyacrylamide Tris-borate-EDTA (TBE) gels containing 8M urea as a denaturant.
How is the extinction coefficient determined?
The extinction coefficients of SOMAmer reagents are determined using the nearest neighbor method for estimation of extinction coefficients of oligonucleotides (Cantor, C.R. et al., Biopolymers, 9, 1059- 1077., Cavaluzzi, M.J. and Borer, P.N., Nucleic Acids Res., 32, e13). The third term in the equation in the references accounts for the proprietary modifications of SOMAmer reagents. Extinction coefficients are determined for each new modified nucleoside (nucleotide) as they are introduced into newly discovered SOMAmer reagents. Sequence-specific extinction coefficients are included on the Certificate of Analysis.
What are the melting temperatures (Tm) of the folded SOMAmer reagent structures?
The selection experiments used to discover SOMAmer reagents were performed at 37°C, so the bound, folded structures of the SOMAmer reagents are stable at this temperature and below. The melting temperatures of the majority of the SOMAmer reagents have been measured in solution without protein present and are 50-65°C. The transitions are typically broader than those observed for double stranded DNA. The bound forms of the SOMAmer reagents are expected to be more stable.
In what buffers are SOMAmer reagents compatible?
SomaLogic recommends reconstitution in deionized water to 50 μL, which will result in 5 mmol HEPES at pH 8.0, 1 mM EDTA, and 10 μM of Reagent. Most buffers near physiological ionic strength and pH should are compatible, but controlled binding experiments in buffers suitable for the intended application are recommended.
What is the composition of SOMAmer reagents?
SOMAmer reagents are synthetic oligonucleotides with standard DNA 2’-deoxynucleotides as well as unique modified nucleotides developed by SomaLogic (see Vaught et. al., JACS, 2010, 132, 4141-4151). In addition, each SOMAmer reagent can be modified with a capture (biotin or amine), conjugation (amine or thiol), or detection moiety (fluorophore) on the 5' end and an inverted dT on the 3’ end. Custom orders may be requested by contacting SomaLogic Sales at email@example.com or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.)
Why are the SOMAmer reagent quantities reported in nmol instead of mg?
SOMAmers are high-affinity binding reagents and this facilitates determination of the quantities needed for experiments. The molecular mass is provided for those who prefer to convert to mass.
SOMAmer reagents are selected using the SELEX (Systematic Evolution of Ligands using Exponential Enrichment) method, starting with libraries of 1015 molecules and iteratively narrowing that number based on affinity of the rounds of SELEX. Usually about 100 sequences are available after 6 – 8 rounds of SELEX that have acceptable affinity to the target. While all of the SOMAmer reagent candidates will bind the target to varying degrees, the properties of these reagents will vary, including their performance in any given application. While one sequence might perform well in one set of conditions, another sequence may perform better in another.
Are there preferred sources of target protein (e.g. recombinant systems, etc.)?
SOMAmers recognize the tertiary structure of proteins, so protein sources that create a properly folded protein are preferred.
Can a custom SOMAmer reagent be designed to discriminate between protein variants or post- translational modifications (PTMs) of the target protein?
SOMAmer reagents that discriminate between protein variants (e.g. highly homologous proteins or mutant forms of the same protein) have been successfully discovered at SomaLogic. Because SOMAmer reagents bind large, conformational epitopes it is difficult to predict ahead of time the chance for success; however there are several examples where this has been achieved with high specificity. Please contact SomaLogic Technical Support at firstname.lastname@example.org or by telephone at 1-800- 324-0783 or 303-625-9000 regarding any specific concerns.
How many libraries are used to identify candidate SOMAmer reagents that bind to the target analyte?
SomaLogic will use up to two differentially modified DNA libraries in the SELEX process to identify SOMAmer reagents that bind the analyte target. Additional libraries are available for an additional fee. Please contact your sales representative or at email@example.com for additional information.
How many SOMAmer binding reagents will be obtained during the custom SOMAmer Discovery Service process?
During the standard process for custom SOMAmer design, we will provide at least 5 nmoles each of 5 candidate SOMAmer binding reagents with Kd values of less than 25 nM (or all candidates meeting this dissociation standard if fewer than 5 are discovered) to the customer for orthogonal testing/validation. Upon selection of one of these SOMAmer reagents by the customer, a single fit-for- purpose SOMAmer reagent will be provided at 50 nmoles. Additional SOMAmer reagents may be purchased at this time for an additional cost; please contact SomaLogic Sales at firstname.lastname@example.org or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000.
How much target protein is required to design a custom SOMAmer reagent?
For standard SOMAmer Discovery Service projects, we request that a minimum of 250 μg of purified protein (in the native, folded form) be submitted. If less than this amount is available, please contact SomaLogic Sales at email@example.com or by telephone at 1-844-SOMAMER (1-844-766-2637) or the main number at 303-625-9000. For projects that entail custom processes, more protein may be requested.
What are acceptable fusion tags on the target analyte?
In general, fusion tags such as polyHis, human IgG1 Fc, and biotin are acceptable. GST and HALO tags are incompatible with the SOMAmer Discovery Service at this time. Please contact SomaLogic Technical Support at firstname.lastname@example.org or by telephone at 1-800-324-0783 or 303-625-9000 regarding other fusion tags of interest.
What are the expected dissociation constants (Kd) for the candidate SOMAmer binding reagents?
SomaLogic will provide at least 5 nmoles each of 5 candidate SOMAmer binding reagents with Kd values of less than 25 nM, or all candidates meeting this dissociation standard if fewer than 5 are discovered. The median affinity for the SOMAmer reagents in SomaLogic’s biomarker discovery assay is 0.9 nM.
What buffers are compatible with the SOMAmer Discovery process (i.e. in what buffers can the target analyte be suspended)?
In general, mild non-denaturing buffers are compatible with the process as long as they do not have an extreme pH (e.g. pH<4 or pH>10) or high detergent content. Denaturing buffers are incompatible with the SOMAmer Discovery Service at this time. Please contact SomaLogic Technical Support at email@example.com or by telephone at 1-800-324-0783 or 303-625-9000 regarding any specific buffer concerns.
What is the minimum size protein target that can be used when designing a custom SOMAmer reagent?
The target protein should be a minimum of 25 amino acids excluding fusion tags (e.g. polyHis, IgG, biotin, etc.). If the target protein of interest is less than 25 amino acids, it may be possible to design a custom SOMAmer reagent, but please contact SomaLogic Technical Support at firstname.lastname@example.org or by telephone at 1-800-324-0783 or 303-625-9000.
Will the epitope on the target analyte be known?
Crystal structure analyses of a small number of SOMAmer reagent-protein complexes indicate SOMAmer reagents bind large, conformational epitopes, but the exact epitope of every SOMAmer reagent is not known.
Frequently asked questions about the SOMAscan assayPlease choose a category below:
SOMAscan assay-specific questions
What analytes are measured in the SOMAscan 1.3k Assay, and are they specific to a certain disease area?
You can download the list of 1,310 analytes here or by emailing a request to email@example.com. The SOMAmer reagents in the assay cover a broad array of proteins associated with cellular processes and disease patho-physiology as shown in the bar chart below. However, please note that this information relies on published scientific literature; for example, because of the emphasis on cancer research, more proteins have been measured and reported in that area than any other. If a particular protein has not been measured in a specific area or it has not been reported in the literature it will be “silent” rather than truly absent.
What controls are used in the SOMAscan assay?
We use both internal calibrator samples that are pooled from multiple individuals and quality control samples that are from a defined population. Calibrator samples are used as a reference standard. Internal quality control samples are also included to ensure that previously measured differences between calibrator and quality control samples are maintained. Spiked analytes are currently not used as a reference in the SOMAscan Assay, although we do this with our smaller panel assays. If the calibrators and QC samples fail, then we assess the assay as a failure.
Are samples assayed "neat"?
Plasma and serum samples are divided into three different dilutions and assigned a set of SOMAmer reagents to each dilution based on empirically detected levels in healthy individuals for that biological matrix. The most abundant proteins are targeted in the 0.005% sample dilution with the 0.005% SOMAmer reagent mix, and the lowest abundance proteins are targeted in the 40% sample dilution with the 40% SOMAmer reagent mix. Non-plasma samples may be divided into different dilutions specific for that matrix. For example, the detection range for a single analyte in human plasma may be at a dilution of 40%, while the same analyte might have an optimized detection range in human CSF at a dilution of 1%.
Why are so many intracellular proteins detected?
In our internal studies, we have found proteins thought to be "intracellular" are present in plasma and serum. It is not uncommon to observe this event. There is a growing body of evidence, and with it heightened interest in, what researchers are calling the "exoproteome.” The exoproteome is defined as a group of proteins that appear in the fluid proximal to a given cellular system and arise from secretion, export, lysis and/or death. Below is a list of several recent publications that outline current thinking and examples of exoproteome research. It is worth noting that this subset of the proteome has only become of real interest as analytical methodologies, such as the SOMAscan Assay, have become more sensitive and reliable in detecting proteins at low levels. References:
- Armengaud, J, Christie-Oleza JA, Clair G, et al. Exoproteomics: Exploring the World Around Biological Systems. Expert Rev. Proteomics. 2012; 9(5):561-575.
- Farrah T, Deutsch EW, Omenn GS, et al. A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas. Mol. Cell. Proteomics. 2011; 10(9): M110.006353. DOIL 10.1074/mcp.M110.006353.
- Hortin G, Sviridov D. The Dynamic Range Problem in the Analysis of the Plasma Proteome. Journal of Proteomics. 2010; 73:629-636.
- Karagiannis GS, Pavlou MP, Saraon P, et al. In-depth Proteomic Delineation of the Colorectal Cancer Exoproteome: Mechanistic Insight and Identification of Potential Biomarkers. Journal of Proteomics. 2014; 103:121-136.
- Perkins, G, et al. Multi-Purpose Utility of Circulating Plasma DNA Testing in Patients with Advanced Cancers. PLoS One. 2012; 7(11): e47020.
- Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011; 11: 426–437. doi: 10.1038/nrc3066.
- Thierry AR, Mouliere F, Gongora C, Ollier J, Robert B, et al. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res. 2010; 38: 6159–6175. doi: 10.1093/nar/gkq421.
- Van Summaren A, Renes J, van Delft JHM, et al. Proteomics in the search for mechanisms and biomarkers of drug-induced hepatotoxicity. Toxicology in Vitro. 2012; 26:373-385.
What is the standard turnaround time for a study?
The standard turn-around time (TAT) for a study is 5 weeks from contract execution and sample receipt to data delivery for most studies (very large studies could take longer). Historically, our average TAT is 34 days. In certain situations, SomaLogic may be able to expedite studies if there are pressing time constraints; please contact your Sales Representative.
How is non-specific binding minimized in the SOMAscan assay?
SOMAmer reagents were designed to have long half-lives (i.e., slow off-rates). Specific interactions between SOMAmer reagents and proteins remain intact while non-specific binding events – which have quick off-rates – are disrupted. The first interaction is when the sample competes for reagent binding during equilibration and the second is when the protein-SOMAmer reagent complex is released back into solution by photocleavage to remove the complex from the streptavidin bead. Kinetic challenge occurs during this photo-cleavage step. The SOMAscan assay takes advantage of the slow off-rates of the SOMAmer reagents by including excess competitor in this photo-cleavage solution; quickly dissociating complexes are prevented from rebinding and specific complexes are selectively enriched.
SOMAscan assay matrix-specific questions
Can samples from non-human species be assayed with the SOMAscan assay (e.g., mouse or rat)?
The SOMAscan assay can reproducibly and reliably measure hundreds of proteins in small sample volumes from mice, rats, cats and dogs better than any available alternative; non-human primates appear to cross-react even more. Using the SOMAscan assay to measure the proteome of non-human species has already led to novel discoveries indicating the SOMAscan assay can oﬀer powerful, unbiased proteomic discoveries leading to deeper biological understanding of these species. Utilizing the same reagents in multiple species and in in vitro studies, creates an opportunity for a single translational platform, minimizing the technical risk of moving between diﬀerent platforms. Each matrix/species is optimized for overall performance of the assay; however at this time, we do not have species-specific panels. The volume of sample required depends upon the number of dilutions (1-3 dilutions per matrix) and the highest concentration for each dilution: the higher the concentration, the more volume is needed.
How does the SOMAscan Assay correlate with immunoassays (ELISAs)?
Based on a small number of comparisons of the SOMAscan Assay to ELISAs, we believe the SOMAscan Assay correlates with ELISAs comparably to the degree that ELISAs correlate with other ELISAs. Please see our Technical Note SSM-005 Correlation of SOMAmer® Reagents in the SOMAscan® Assay and Commercially Available Immunoassays for additional details.
Can the SOMAscan assay be run with my matrix?
We request that you provide the details about your matrix, including the sample collection and processing protocols, for our technical specialists to review. Sample preparation must preserve the native, folded structure of the protein and the sample should not contain DNA-binding substances. During this review our team will look for substances that may interfere with the assay. After the feasibility review, it may be possible that we can assay your matrix according to our already defined protocols or we may need to discuss a new matrix feasibility assessment.
SOMAmer reagent questions (specific to SOMAscan assay)
How did SomaLogic select the SOMAmer reagents for the SOMAscan assay?
We selected the SOMAmer reagents based upon the following criteria: 1) Proteins that were thought to be present in human plasma or serum, or expressed in a wide variety of conditions. 2) Commercially available human proteins, whether or not they were known to be expressed in plasma or serum. 3) A SOMAmer reagent identified that bound with Kd < 10 nM and passed subsequent QC criteria. Larger Kd values may be permitted for highly abundant analytes.
Can the SOMAmer reagents selectively bind proteins that have post-translational modifications (PTM)?
SOMAmer reagents bind proteins in their folded forms. If a post-translational modification alters the structure of a protein or occludes the binding of a SOMAmer reagent, we may be able to generate SOMAmer reagents that differentiate between the different protein forms. However, in the absence of a structural change, a SOMAmer reagent will likely bind both forms equivalently.
Can SOMAmer reagents bind small proteins/polypeptides?
SOMAmer reagents bind natively folded proteins. It is challenging to generate SOMAmer binding reagents to the shorter polypeptides because they are typically more flexible and may not hold a stable structure. The more flexible the protein the more challenging it is to generate SOMAmer reagents because our SOMAmer reagents recognize stable tertiary structures. Within the SOMAscan assay menu there are SOMAmer reagents that bind to small polypeptides, in the <5 kDa range, such as insulin, b-endorphin, BNP-32, glucagon, etc.
How are the SOMAmer reagents characterized before inclusion into the SOMAscan assay menu?
Reagents are qualified for use in the SOMAscan assay if the apparent Kd for the selected protein is 1x10-9 M or better, the RFU range is > 1.5 logs, and the captured band from the selected protein preparation is consistent with the intended target. The typical Kd value for a SOMAmer reagent is well in the sub-nanomolar range as determined by a solution binding method. We incubate the binding protein in with the SOMAmer reagent and determine the amount of complexes that are formed in a solution binding method where we capture the complexes through a tag or through a non-specific interaction. These are not determined by a method like surface plasmon resonance (SPR), so surface effects are not involved.
Can you make a SOMAmer reagent that will recognize a protein complex?
Yes. Selections have sometimes been performed against individual components or the complex and then tested against the complex. Please contact your Sales Representative for further information.
How many samples are recommended per treatment group?
This depends on numerous variables: It is always recommended to consult a statistician on all aspects of study design. In the absence of such a consultation, we offer the following guidance: The number of samples per group depends on the expected size of the physiological effect, the variation in the population to be tested, as well as other experimental parameters. The SOMAscan Assay is a discovery tool for hypothesis generation and is typically used to discover new biomarkers that can be further tested in follow-up validation studies. In animal studies using genetically identical strains that are housed similarly, the variability is expected to be less than the variability within a group of humans. The median assay CV for the SOMAscan Assay is 5%. The variability of sampling genetically identical animals is approximately 3-5%. Combined, this results in an estimated CV of 8 - 10%. Suggested sample size estimates of animals per group (unpaired, with 8% - 10% CVs) as a function of effect size is shown in the table below.
If the samples are paired (drawn from the same animal over time or after treatment) the number of animals per group can be fewer. The number still depends on variables that require statistical analysis, but ideally, there should be a minimum of 8-10 animals per treatment group.
|Effect Size (% change)||# Animals per Group|
How many repeated measurements per individual do I need for a time course or dose response of cell treatment?
This depends on numerous variables: It is always recommended to consult a statistician on all aspects of study design. In the absence of such a consultation we offer the following guidance: The number of repeated measurements per individual required for a study depends on the expected physiological effect size, the variation in the population to be tested, as well as other experimental parameters. The SOMAscan assay is a discovery tool for hypothesis generation and is typically used to discover new biomarkers. If the effect size is known to be large (> 2-fold), then fewer samples per group can be used. For cell studies, our bioinformaticians recommend biological triplicates (n = 3) or greater, whenever possible. If there is a time course and the number of samples must be limited due to budget, our recommended strategy is to reduce the number of samples at interior time points or doses to duplicates (n = 2), while retaining triplicate measurements (n = 3) for the time points/doses expected to vary the most from control. If a certain data point is critical for the experiment it should be run in triplicate or greater (n ≥ 3). This is illustrated in the tables below:
|Cell Line A|
|24hrs||2 or 3||2 or 3||2 or 3||2 or 3||8 or 12|
|Grand Total||23 - 27|
|Cell Line A|
|12hrs||2 or 3||2 or 3||2 or 3||2 or 3||8 or 12|
|24hrs||2 or 3||2 or 3||2 or 3||2 or 3||8 or 12|
|Grand Total||31 - 39|
Do I need to include a media control sample?
It depends on the study question that is being asked. If you want to know what is secreted or consumed by the cells over time, then it is recommended to include a media control sample. If your question is primarily about the effect of treatment compared to a vehicle control, then it is unnecessary.
What are the best time points for my study?
It is recommended to use a previously known measure to estimate the best time points for your study. If nothing else is known, a cell viability measurement over a time course upon stimulation with drug can help to determine the answer. Example data from previous studies:
|Sample Type||Dose||Time||Approximate # of analytes below FDR cutoff, p-value < 10-4.4. (5%/10%)||# analytes with ³ log2 fold change below 10% FDR|
|Lysate (four studies)||>1uM||24hrs||14, 16, 37 and 42 (5%)|
How do I bridge previous sample runs to new runs?
Please contact SomaLogic to speak with one of our scientists.. Established calibration methods using endogenous pooled sample 'calibrator' references have been shown to reduce run-to-run variance on replicate samples. It has also been shown to improve consistency of run-to-run distributions of clinical samples provided the assumptions of data standardization (including randomization of clinical samples across plates) are met. We also run quality control samples (replicate samples from distinct populations) that are not used in data standardization and, therefore, may be used to evaluate post-calibration plate bias. As time between runs increases, the opportunity increases for changes to occur in the assay that impact signal intensity and decrease the efficacy of standard calibration methods. Assay changes include necessary changes in consumable reagents (buffers, beads, control sample lots, SOMAmer reagent master mix) as well as assay protocol or instrumentation changes implemented to improve assay performance. We strongly recommend designating a group of samples as bridging samples whenever one study is to be tied to another study. These bridging samples should represent the independent groups or clinical populations that will be directly compared between studies. Including a set of bridging samples allows a direct comparison across the studies with a set of replicate clinical samples from the particular population/s of interest. Though this procedure mirrors our internal QC procedure, by using replicate clinical specimens a client will be in a better position to defend findings that arise from comparisons between independent sample groups assayed in different studies. In either case our QC samples provide an internal check that the inter-study calibration performed as expected.
Reproducibility and interpretation of SOMAscan results
What is the inter-assay variability between runs?
The SOMAscan assay has been well characterized for reproducibility with respect to inter-assay variation between runs. The SOMAscan assay has excellent reproducibility, of the 1310 SOMAmer reagents, the median total %CV is ~5% and 98% of the SOMAmer reagents have a median %CV of 15% or lower in plasma.
Does SomaLogic run disease-specific controls to evaluate disease sample/analyte reproducibility?
We cannot run these in the context of disease samples such as in plasma or serum because we traverse all diseases. However, we have evaluated the inter-run reproducibility of all proteins measured by the SOMAscan Assay where SOMAmer reagents have a median total %CV of ~5%.
How does SomaLogic report data?
We report differential protein regulation in RFU space as the SOMAscan Assay was designed for discovery purposes.
Are RFUs linearly proportional to the amount of protein present so that for a given protein, there is twice as much of that protein present in a sample with RFU 4000 vs. a sample with RFU 2000?
Relative florescence units (RFU) are a relative measure of protein quantity, which is a function of the unique characteristics (affinity, on-rate, off-rate) of each specific SOMAmer reagent as well as the assigned mix dilution. A two-fold change in signal may not be representative of a two-fold change in protein concentration. However, it is appropriate to compare the RFU values for a specific analyte across all samples, which is the basis for most discovery analyses.
How is your data standardization controlled for quality?
A SOMAscan quality statement is delivered with each set of SOMAscan Assay results. Our data standardization procedure, which is designed to remove assay bias or batch effects, is composed of three main steps. The first step is hybridization normalization, which utilizes a set of control SOMAmer reagents added to each sample prior to hybridization in order to remove hybridization biases. The second step is median normalization and is designed to remove possible biases between samples due to variation in the assay, such as differences in liquid handling. The third step, “calibration,” removes inter-plate biases using a set of internal control replicate samples. The delivered data have undergone both of these normalization steps. Additional details and the acceptance criteria of each of these steps can be provided upon request. Please contact us.
What was the distribution of the hybridization normalization scale factors and the distribution of the median normalization scale factors?
Hybridization and median normalization scale factors for each sample are included in the delivered ADAT data files. Hybridization scale factors are under the "HybControlNormScale" column heading and median normalization scale factors under the "NormScale_<dilution>" column heading in the ADAT file.
The relation between Dilution Linearity Range, Assay %CV, and F-Statistic (Mixed) is unclear; can you explain?
Each of these is an independent metric calculated to give some information about assay performance. Any one of these metrics, alone, may be sufficient for a scientist to gain confidence in the assay depending on the individual’s requirements. Dilution Linearity Range (DLR) is a count of the number of points from a 16-point 2-fold titration series that fall within 25% of the expected value. The DLR may provide confidence because 1) this is the most straightforward metric of expected behavior when the protein is present and the SOMAmer reagent is capturing the protein and 2) linear behavior is ideal to make direct statements about protein concentration based on RFU readings. %CV is the primary metric for assay reproducibility and this metric is very consistent across different matrices and species and is the only one of the three (%CV, DLR, F-stat) that is not strictly dependent on the population/samples used in the qualification experiment. For this reason, some scientists rely on reproducibility metrics such as %CV alone and do not use the other two (DLR, F-stat) in their evaluation of the assay. F-stat informs whether the small population tested has some variance above assay variance. Stated another way, F-stat informs us whether the SOMAmer reagent is ‘signaling’ in the population tested. The F-stat gives us information about the matrix/species rather than about the SOMAmer reagent performance but is useful to get a general idea of the expected number of proteins in the menu that may be measured differentially among a set of individuals. The population variance is established with a small population of healthy individuals and therefore not representative of the population in a clinical setting. None of these metrics is definitive regarding the absolute performance of a SOMAmer reagent or of the assay. For example, DLR is based on unit linear behavior, which is not strictly necessary for an assay reagent to have excellent performance. Another particular issue is that the population selected for a future experiment may be very different from the samples/population used for the titration and F-statistic experiments. For these reasons, we combine these independent metrics into the Qualitative Score to make our most conservative statement about the matrix based on the experiments run.
Do you offer statistical support?
We can provide statistical support; the costs may depend on the study and analysis requirements. Please contact your SomaLogic Sales Representative for details.
Can we get the data in an Excel file or a file compatible with statistical analysis software?
The ADAT file is compatible with a variety of software tools. To open the file in Excel, do the following: File, Open, browse to the file location, select All Files (*.*) and double-click on the file. Follow the Text Import Wizard prompts or simply select Finish since the default settings conform to the ADAT file configuration.