The Wide World of ASMS: Applications of ASMS Screening for Therapeutic Innovation

What is ASMS?

Affinity selection mass spectrometry (ASMS) is a powerful technique that enables high-throughput screening of small molecule compounds against a wide range of targets. This technology offers several key advantages, including broad target compatibility, minimal assay development, and no requirement for target or compound labeling. In a typical ASMS experiment, compound libraries are screened against a protein target of interest to identify promising binders. However, ASMS is also extremely well suited for the screening of more specialized target types, such as RNA and DNA oligos, protein complexes, and leads for targeted degrader development. In this post, we will explore how ASMS can be used to drive drug discovery and development projects across a range of targets and modalities, highlighting its utility as a high-throughput screening approach.

If you’re new to ASMS and would like to learn more about its core benefits, check out this blog post by our Founder and CEO, Can Ozbal.

ASMS for RNA & DNA Targets

One notable application of ASMS is for the discovery of small molecules that bind RNA or DNA targets. These oligonucleotide targets can be challenging to interrogate using other methods; for example, fluorescent reporter screens are prone to off-target effects and high false positive rates, while DEL screening is vulnerable to artifacts arising from interactions between the target oligo and DEL tags. In contrast, RNA and DNA targets can be readily screened using solution-phase ASMS, which avoids the need for target or compound labeling and maintains the conformational flexibility of the target.

Indeed, ASMS has been successfully used to identify small molecules that bind a number of RNA and DNA targets. For example, one research group screened 42 RNA species using ASMS, and their efforts identified 944 compounds that were selective to a single RNA target. This report highlights the power of ASMS in identifying novel and selective binders against a diverse range of RNA targets. A similar approach was used to identify binders of the G-quadruplex DNA structure, validating the further applicability of this technology to DNA oligo targets.

ASMS for Protein Complexes

ASMS is also well suited for the screening of multi-protein complexes, as well as protein:DNA or protein:RNA complexes. Because this technique can be performed in solution and without target labeling, tagging, or immobilization, native interactions between complex subunits are readily preserved. A coupled screening/counter-screening strategy, in which a protein complex and its individual subunits are screened in parallel, can be used to facilitate the identification of complex-specific binders; a similar approach (to be explored further in next month’s blog!) also empowers the discovery of molecular glue candidates.

The flexibility of ASMS to screen complex targets enables new frontiers of pharmaceutical innovation. This approach can confer increased specificity compared to targeting of a single factor, potentially offering a clinical advantage by reducing off-target effects. For example, researchers seeking to understand the mechanism underpinning SMN2 splicing modulators for the treatment of spinal muscular atrophy discovered that these small molecules bind a ribonucleoprotein (RNP) complex specific to SMN2 and STRN3 splicing. Drugs targeting this unique complex interface can potently and selectively modulate splicing of target transcripts without impacting splicing broadly. Protein complexes can also be targeted by small molecules that disrupt (or strengthen) protein-protein interactions, with wide-ranging therapeutic applications.

ASMS for Targeted Degrader Development

Another powerful application of ASMS screening is for the discovery and development of targeted degraders. This therapeutic modality leverages endogenous cellular machinery to induce the selective degradation of target proteins. While PROTACs are the most well-known representative of this category, variants such as LYTACs, AbTACs, and activatable PROTACs have shown therapeutic promise, and the field continues to expand with ongoing technological advances. As the first round of PROTACs progress through clinical trials to FDA approval, this modality offers new hope for the targeting of previously undruggable proteins.

ASMS enables the high-throughput screening and identification of target-specific ligands, which can then be developed into potent and selective degraders. This approach is also valuable for the discovery of novel E3 ligase ligands, which can be used to recruit degradation-inducing machinery in bifunctional degraders. Following the initial identification of screening hits, ASMS can be used to determine and rank binding affinities, enabling the prioritization of leads for development. Indeed, this approach can be used to validate and rank-order hits determined by alternative primary screens, such as DEL screening or functional screening. In this way, ASMS serves as a valuable orthogonal assay for hit confirmation and follow-up.

Why ASMS?

Whether you’re interested in straightforward screening of small molecules against a target protein, or in one of the more specialized applications described above, ASMS is an excellent choice to advance therapeutic discovery and development projects. This solution-phase approach is suitable for a diverse range of target classes, avoids the need for target or compound labels, and can readily screen hundreds of thousands of compounds in just days using pooled approaches. Minimal assay development is required, making ASMS an efficient and effective method for both high-throughput screening and orthogonal hit validation/follow-up. At Momentum, our scientists have extensive experience leveraging ASMS for a range of screening and confirmation applications, including both routine and niche workflows, and are ready to help you leverage this powerful technology towards your own research goals

To get in touch with our team and explore how ASMS can help you identify, prioritize, and optimize small-molecule ligands for a wide range of pharmaceutical applications, send us a message through our contact form.

Make sure you check back next month, where we’ll explore even more applications of ASMS screening for the discovery and development of molecular glues, radiotherapeutics, and membrane proteins!

Sources

Békés M, Langley DR & Crews CM. PROTAC targeted protein degraders: the past is prologue. Nat Rev Drug Disc 21, 181-200 (2022).

Cai Z, Ma H, Ye F, Lei D, Deng Z, Li Y, Gu R & Wen H. Discovery of RNA-Targeting Small Molecules: Challenges and Future Directions. MedComm 6, e70342 (2025).

Chen Q, Li Y, Lin C, Chen L, Luo H, Xia S, Liu C, Cheng X, Liu C, Li J & Dou D. Expanding the DNA-encoded library toolbox: identifying small molecules targeting RNA. Nucleic Acids Res 50, e67 (2022).

Chen Y, Zhang L, Fang L, Chen C, Zhang D & Peng T. Modular Development of Enzyme-Activatable Proteolysis Targeting Chimeras for Selective Protein Degradation and Cancer Targeting. JACS Au 4, 2564-2577 (2024).

Cotton AD, Nguyen DP, Gramespacher JA, Seiple IB & Wells JA. Development of Antibody-Based PROTACs for the Degradation of the Cell-Surface Immune Checkpoint Protein PD-L1. J Am Chem Soc 143, 593-598 (2021).

Dueñas ME, Peltier-Heap RE, Leveridge M, Annan RS, Büttner FH & Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 15, e14850 (2022).

Flusberg DA, Rizvi NF, Kutilek V, Andrews C, Saradjian P, Chamberlin C, Curran P, Swalm B, Kattar S, Smith GF, Dandliker P, Nickbarg EB & O’Neil J. Identification of G-Quadruplex-Binding Inhibitors of Myc Expression through Affinity Selection-Mass Spectrometry. SLAS Discov 24, 142-157 (2019).

Foley TL, Burchett W, Chen Q, Flanagan ME, Kapinos B, Li X, Montgomery JI, Ratnayake AS, Zhu H & Peakman M-C. Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries. SLAS Discov 26, 263-280 (2021).

Ma Z & Zhou J. NDA Submission of Vepdegestrant (ARV-471) to U.S. FDA: The Beginning of a New Era of PROTAC Degraders. J Med Chem 68, 14129-14136 (2025).

Martin WJ, Grandi P & Marcia M. Screening strategies for identifying RNA- and ribonucleoprotein-targeted compounds.Trends Pharmacol Sci 42, 758-771 (2021).

Nada H, Choi Y, Kim S, Jeong KS, Meanwell NA & Lee K. New insights into protein-protein interaction modulators in drug discovery and therapeutic advance. Sig Transduct Target Ther 9, 341 (2024).

de Oliveira PCO, do Amaral BS, Cardoso CL, Cass QB & De Moraes MC. Breaking the boundaries of affinity selection-mass spectrometry: From ligand screening to target-ligand interaction insights. J Pharm Anal 101379, (2025).

Prudent R, Annis DA, Dandliker PJ, Otholand J-Y & Roche D. Exploring new targets and chemical space with affinity selection-mass spectrometry. Nat Rev Chem 5, 62-71 (2021).

Prudent R, Lemoine H, Walsh J & Roche D. Affinity selection mass spectrometry speeding drug discovery. Drug Disc Today 28, 103760 (2023).

Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim H-Y, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker, Smith GF & Nickbarg EB. Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry. ACS Chem Biol 13, 820-831 (2018).

Rizvi NF, Santa Maria JP Jr., Nahvi A, Klappenbach J, Klein DJ, Curran PJ, Richards MP, Chamberlin C, Saradjian P, Burchard J, Aguilar R, Lee JT, Dandliker PJ, Smith GF, Kutchukian P & Nickbarg EB. Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space. SLAS Discov 25, 384-396 (2020).

Rodríguez-Gimeno A & Galdeano C. Drug Discovery Approaches to Target E3 Ligases. ChemBioChem 26, e202400656 (2025).

Sivaramakrishnan M, McCarthy KD, Campagne S, Huber S, Meier S, Augustin A, Heckel T, Meistermann H, Hug MN, Birrer P, Moursy A, Khawaja S, Schmucki R, Berntenis N, Giroud N, Golling S, Tzouros M, Banfai B, Duran-Pacheco G, Lamerz J, Liu YH, Luebbers T, Ratni H, Ebeling M, Cléry A, Paushkin S, Krainer AR, Allain FH-T & Metzger F. Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers. Nat Commun 8, 1476 (2017).

Ye Q, Belabed H, Wang Y, Yu Z, Palaniappan M, Li J-Y, Kalovidouris SA, MacKenzie KR, Teng M, Young DW, Fujihara Y & Matzuk MM. Advancing ASMS with LC-MS/MS for the discovery of novel PDCL2 ligands from DNA-encoded chemical library selections. Andrology 11, 808-815 (2023).

Zheng Q, Guo J, Ma R & Pu W. Lysosome-targeting chimera (LYTAC): A silver bullet for targeted degradation of oncogenic membrane proteins. MedComm Oncol 3, e64 (2024).

Zhong G, Chang X, Xie W & Zhou X. Targeted protein degradation: advances in drug discovery and clinical practice. Sig Transduct Target Ther 9, 308 (2024).