Activity-Based Protein Profiling (ABPP-MS) Services

When your team needs to know not just whether a protein is present, but whether it is functionally active, engaged by a probe, or displaced by a compound, Activity-Based Protein Profiling becomes much more informative than indirect validation alone. We use ABPP-MS to help drug discovery teams generate active-state evidence that can support selectivity analysis, inhibitor profiling, and project-level decisions.

Our MassTarget platform brings together multiple ABPP routes so we can match the workflow to the question you actually need to answer. That gives you a practical path for competitive profiling, covalent inhibitor evaluation, enzyme-family analysis, and active-state target support in complex biological systems.

Active-state target evidence
Competitive and selectivity support
Route-matched ABPP workflows
Built for discovery decisions

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Activity-Based Protein Profiling ABPP-MS service overview for drug discovery

What ABPP ShowsWhy It MattersCapabilitiesMethod SelectionServices We OfferWorkflowDeliverablesSampleDemoCase StudyFAQ

What ABPP-MS Can Show You in Drug Discovery

Activity-Based Protein Profiling is designed for one of the most important problems in drug discovery: knowing whether a compound is affecting proteins in a way that matters functionally. Instead of measuring only abundance, ABPP uses activity-based probes to track proteins in their active or probe-accessible state. That makes the output especially useful when your team needs to understand inhibitor engagement, enzyme-family behavior, competitive displacement, or selectivity across related proteins.

In practical terms, ABPP-MS can help answer questions such as whether an inhibitor is engaging functionally relevant proteins, whether a compound displaces probe labeling in a meaningful way, how selective the chemistry is across related enzymes, and whether the signal supports moving a compound forward.

This is why ABPP is especially valuable for covalent inhibitor programs, active-site chemistry, and enzyme-directed projects. Public literature consistently frames ABPP as a chemical proteomic strategy for characterizing enzyme function directly in native biological systems and for supporting inhibitor discovery and evaluation. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry Activity-Based Protein Profiling (ABPP) of Cellular DeISGylating Enzymes and Inhibitor Screening

Why active-state evidence changes the decision

A protein can be present without being functionally important in the moment you are testing. ABPP helps close that gap by focusing on proteins in a probe-accessible or active state, which often makes the result more useful for inhibitor and selectivity decisions.

What ABPP can reveal that abundance data cannot

Standard proteomics may tell you that a protein exists in the sample. ABPP can help show whether the active population of that protein is affected, competed, or selectively engaged.

Where ABPP fits in discovery-stage projects

ABPP is especially relevant for covalent inhibitor profiling, enzyme-family questions, competitive engagement studies, and projects where active-state evidence matters more than simple presence-or-absence data.

Why Teams Choose ABPP Instead of Conventional Validation Alone

Conventional validation methods still matter, but they often leave key uncertainties unresolved. Pull-down experiments, Western blot follow-up, and functional assays can all be helpful, yet they may not tell you whether your chemistry is acting on the active fraction of a target, how broadly the effect extends across related proteins, or whether a probe displacement pattern supports real selectivity.

We use ABPP when those questions start affecting project decisions. If your team needs to compare inhibitor behavior, understand enzyme-family selectivity, or add a more direct engagement layer to a mechanism story, ABPP is often the most practical next step.

When pull-down or phenotype data is not enough

A pulled-down protein is not always the most relevant functional protein, and a phenotypic response is not always explained by direct active-state engagement. ABPP provides a more function-aware layer of evidence.

When selectivity becomes the real question

As discovery programs mature, the question often shifts from "does it work?" to "what else is it affecting?" ABPP is especially useful at that stage because it can support competitive and selectivity-oriented interpretation across related proteins or enzyme classes.

When an inhibitor program needs stronger engagement support

For inhibitor programs, especially covalent or probe-dependent ones, ABPP can provide stronger support than indirect biology alone by showing how active-state labeling changes in response to chemistry.

How this connects to neighboring routes

When the project needs target deconvolution or residue-level mapping instead, Photoaffinity Labelling (PAL-MS) or Reactive Residue Profiling may be the better route.

Our ABPP-MS Capabilities Across Active-State, Competitive, and Selectivity Questions

We do not treat ABPP as one fixed experiment. The best route depends on the chemistry, the sample context, the biological question, and the kind of evidence your team needs.

Our ABPP capabilities can support active-state profiling, competitive engagement, enzyme-family analysis, and broader route extension across the chemoproteomics portfolio.

ROUTE 1

Competitive and target-engagement-focused ABPP routes

When the core question is whether a compound competes with an activity-based probe in a meaningful way, we generally guide projects toward competitive ABPP logic.

ROUTE 2

Global, live-cell, and enzyme-family-specific ABPP routes

When the need is broader functional profiling, cellular context, or a focused enzyme-family question, global, live-cell, or enzyme-family-specific ABPP routes often provide a better fit.

ROUTE 3

How we support project design and result interpretation

We help align the ABPP route, chemistry logic, sample plan, QC review, and deliverable structure with the decision your team needs to make, rather than simply running a standard template experiment.

ROUTE 4

How ABPP can extend into broader evidence chains

A good ABPP study can support follow-up choices across the wider MassTarget portfolio when your project needs broader chemoproteomics, target deconvolution, or orthogonal protein-state evidence.

How to Choose the Right ABPP Route for Your Project

The most important question on this page is not whether ABPP is useful in general. It is whether the right ABPP route is being matched to your project.

Method	Main question answered	Best suited for	Key strengths	Main limitations
Competitive ABPP	Does a compound displace probe labeling in a functionally meaningful way?	Target engagement, selectivity analysis, inhibitor comparison	Strong for competitive engagement and compound ranking	Depends on probe fit and competitive assay design
Global ABPP (LC–MS/MS)	How does active-state behavior change across a broader protein set?	Broader active-state profiling and discovery-stage comparison	Useful for wider functional context	Interpretation may be broader than a focused target question needs
Live-cell ABPP	Does active-state engagement occur in a cellular context?	Cell-context studies and intracellular interpretation	Adds biologically relevant context	Sample handling and probe behavior become more critical
Enzyme-Family-Specific ABPP	How does chemistry behave across a defined enzyme family?	Focused biology and class-level selectivity questions	Well suited to family-specific prioritization	Less useful for broad target-deconvolution questions
Covalent Inhibitor Profiling	How selective and convincing is a covalent inhibitor program?	Covalent chemistry, warhead evaluation, inhibitor prioritization	Highly relevant to discovery-stage covalent decisions	Best interpreted together with chemistry and probe logic
PAL-MS	Which targets are captured by a photoactivatable probe?	Target deconvolution and interaction capture	Useful when direct capture in complex systems is needed	Probe design strongly affects outcome
Reactive Residue Profiling	Which residues or residue classes are engaged or perturbed?	Site-level evidence and residue-centric selectivity analysis	Strong for residue-aware interpretation	Not always the best first route for active-state enzyme questions

Competitive ABPP for engagement and selectivity

Choose Competitive ABPP when the key question is whether probe labeling is displaced in a way that supports target engagement and selectivity interpretation.

Global and live-cell ABPP for broader functional context

Choose Global ABPP (LC–MS/MS) or Live-cell ABPP when a broader or more cellularly relevant view of active-state behavior is needed.

Enzyme-family-specific ABPP for focused biology questions

Choose Enzyme-Family-Specific ABPP when the main question sits at the family level rather than at the level of one target or one residue.

When ABPP is not the best route

If the main need is target deconvolution through direct capture, Photoaffinity Labelling (PAL-MS) may be stronger. If the main need is residue-level mapping, Reactive Residue Profiling may be more appropriate.

ABPP-MS Services We Offer

Competitive ABPP — best when your team needs direct competitive engagement and selectivity interpretation.
Isotope Labeling–Based Quantitative ABPP — best when quantitative comparison across conditions is central to the project.
Bioorthogonal Labeling–Based Target Identification — best when target identification requires a click-chemistry-compatible labeling route.
Global ABPP (LC–MS/MS) — best when your project needs a broader active-state proteome readout.
Live-cell ABPP — best when cellular context is central to the interpretation.
Enzyme-Family-Specific ABPP — best when the question is focused on a specific enzyme class.
HT-ABPP Platform — best when higher-throughput route extension is needed.
Covalent Inhibitor Profiling — best when the chemistry is covalent and selectivity burden matters.

Workflow from Project Intake to Decision-Ready Outputs

We build ABPP-MS projects from the project question backward so the route, chemistry, and outputs stay aligned with the decision your team needs to make.

Project review, probe or chemistry fit, and sample planning

We begin by reviewing your compound or probe, the biological system, the main hypothesis, and the type of output your team needs. At this stage, we determine whether competitive ABPP, global ABPP, live-cell ABPP, enzyme-family-specific ABPP, or a neighboring chemoproteomics route is the best fit.

Labeling, enrichment, LC-MS/MS readout, and quantification

Once the route is set, the technical workflow proceeds through treatment or labeling, enrichment or capture where appropriate, proteomic sample preparation, LC-MS/MS analysis, and quantitative signal extraction. Public ABPP literature consistently describes ABPP as a probe-based workflow that links activity-state labeling to mass spectrometry readout for inhibitor and enzyme-function studies. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry Activity-Based Protein Profiling (ABPP) of Cellular DeISGylating Enzymes and Inhibitor Screening

QC review, interpretation, and final reporting

We review chemistry compatibility, sample integrity, enrichment behavior, MS signal quality, and interpretation thresholds before final reporting. The goal is not just to generate a target list. The goal is to generate outputs your team can actually use in a decision setting.

What Data You Receive and How We Structure Deliverables

A strong ABPP project should end with more than raw signal and a short hit list. We structure deliverables so they can support internal review, selectivity comparison, and next-step planning.

Active-state and competition-oriented result outputs

Depending on the route, a typical package may include competitive displacement views, active-state profiling summaries, ranked protein or enzyme-family outputs, route-specific interpretation tables, and project-level comments.

Raw and processed data for internal review

We support delivery of raw and processed outputs so your internal team can review, compare, and reuse the results if the project expands into follow-up work.

How outputs support prioritization and next-step planning

A good ABPP package should help your team decide whether to advance a compound, refine a probe, shift into a different ABPP route, or connect the project to a broader chemoproteomics or orthogonal MS workflow.

Bioinformatics and data interpretation

Once signals are quantified, we organize the results into a framework that helps your team distinguish strong active-state or competition evidence from weak, ambiguous, or non-actionable observations. That may include ranked target summaries, competition-aware comparisons, enzyme-family-level pattern review, and route-specific interpretation notes.

Sample Planning Considerations for ABPP-MS Projects

Sample type	Typical starting amount	Concentration or quality target	Preparation notes	QC focus
Purified protein target	About 50–200 μg	About 1–10 μM, with high purity preferred	Use MS-compatible buffer conditions and provide known tags or construct information where applicable	Purity, chemistry compatibility, recoverability
Protein complex or enriched fraction	About 100–300 μg	About 1–5 μM, with strong sample integrity preferred	Native-compatible preparation is preferred when route design requires preserved functional state	Complex stability, concentration, route fit
Cell-based or lysate-derived sample	Project-dependent total protein or cell input	Defined probe or inhibitor compatibility required	Keep treatment conditions consistent and avoid strongly interfering buffers	Background control, treatment consistency, labeling quality
Probe or compound submission	Project-specific amount or concentrated stock	Stable formulation and clear structure information required	Provide solvent, stability, and handling details before route confirmation	Chemistry integrity and assay feasibility

Demonstrated Results: Typical ABPP-MS Output Types

Typical ABPP-MS output types for drug discovery

Competitive engagement or displacement result view

This kind of result is typically shown as a comparative signal plot or heatmap that reveals whether probe labeling is displaced in a way consistent with engagement. Teams often use this type of output when comparing compounds or ranking inhibitors by selectivity logic.

Enzyme-family or active-state profiling output

This output usually appears as a grouped profiling view or ranked active-state summary across related proteins. It is especially useful when the project is trying to understand family-level rather than single-target behavior.

Prioritized interpretation summary

This is the most decision-ready output type. It condenses the technical results into a clearer next-step view so teams can discuss prioritization, route expansion, or additional validation work more efficiently.

Published Example: ABPP in Inhibitor Screening and Active-State Enzyme Analysis

Activity-Based Protein Profiling (ABPP) of Cellular DeISGylating Enzymes and Inhibitor Screening

Background

Inhibitor programs often need more than general protein detection. They need a way to measure enzyme activity in a functionally meaningful state and determine whether inhibition can be tracked in a biologically relevant system. A recent ABPP study on cellular deISGylating enzymes provides a useful example of this type of workflow.

Methods

The study used an interferon-stimulated gene 15 activity-based probe to profile deISGylating enzymes in cells. The workflow was designed in both manual and semi-automated formats to support medium- to high-throughput inhibitor screening. Western blotting and proteomics-based methods were used as the main analytical readouts.

Results

According to the published abstract, the workflow provided information on endogenous deISGylating enzyme expression and activity in cells. The reported enzyme panel included USP18 together with several constitutively expressed deubiquitinases that showed cross-reactivity to ISG15, specifically USP5, USP14, USP16, and USP36. The abstract also states that the ISG15-ABPP workflow enabled identification and characterization of potent and selective deISGylating enzyme modulators. These details strengthen the value of ABPP in inhibitor-screening programs because they connect probe-based active-state profiling directly to enzyme activity and modulator characterization.

Conclusion

This example shows how ABPP can support inhibitor programs by linking active-state enzyme analysis, selectivity-related interpretation, and modulator characterization in a cellular setting. For discovery teams, that kind of output can be much more useful than indirect biology alone when the next step depends on functional evidence.

ABPP inhibitor screening and active-state enzyme analysis representative case image

FAQ

Frequently Asked Questions

Q: What makes ABPP-MS different from conventional chemoproteomics workflows?

ABPP-MS is especially useful for active-state and competitive questions, rather than only general target or residue mapping.

Q: When should I choose competitive ABPP instead of PAL-MS?

Choose competitive ABPP when the main question is probe displacement, target engagement, or selectivity. Choose PAL-MS when the project needs direct target capture or deconvolution.

Q: Can ABPP-MS support covalent inhibitor profiling?

Yes. It is especially useful when covalent chemistry and selectivity interpretation are central to the program.

Q: Is ABPP useful for enzyme-family-level selectivity questions?

Yes. That is one of the reasons enzyme-family-specific ABPP routes are valuable in discovery-stage projects.

Q: What kinds of probes and samples are usually compatible?

That depends on the route, but common starting points include purified proteins, complexes, lysates, cell-based systems, and project-specific probes or inhibitors.

Q: What deliverables should I expect from an ABPP-MS project?

Typical outputs include competition-aware result views, ranked protein or enzyme-family summaries, processed quantitative tables, and structured interpretation-ready reports.

Q: How do I know whether ABPP is the right route for my project?

That depends on whether your main need is active-state or competitive evidence. If the project needs direct target capture or residue-level mapping, another chemoproteomics route may be better.

Q: Can ABPP outputs connect to broader chemoproteomics or orthogonal MS workflows later?

Yes. ABPP is often most useful when it feeds into a broader evidence chain for target engagement, selectivity, or mechanism follow-up.

References

Plan your ABPP study with the MassTarget team

Share your probe, chemistry, sample context, and project question, and we will help you choose the ABPP workflow that best fits your next decision point.

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Disclaimer: All products and services provided by Creative Proteomics are for research use only. They are not intended for use in diagnostic, therapeutic, or clinical procedures.

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