Can TPP work with cells, lysates, and tissues?

Yes. TPP can be planned around intact cells, lysates, tissues, and selected complex matrices when the project design and material quality are appropriate.

How many replicates should be prepared for a TPP study?

For most TPP projects, at least three biological replicates per group are preferred to improve reproducibility and interpretation confidence.

Thermal Proteome Profiling (TPP) Service

Q: When should I choose 2D-TPP instead of standard TPP?

2D-TPP is more suitable when stronger concentration-dependent evidence, analog comparison, or clearer compound-ranking logic is needed. Standard TPP is usually the better first step for target deconvolution.

Reveal proteome-wide target engagement, off-target signals, and mechanism clues in native biological systems.

When you need to move from an active phenotype to real protein targets without redesigning your compound, we use thermal proteome profiling to keep the biology as close to its native state as possible.

Our TPP service combines controlled thermal challenge, high-resolution LC-MS/MS, and practical data interpretation to show which proteins change stability after compound treatment, which targets are most likely involved, and where selectivity risks may appear.

We support projects that need proteome-wide target deconvolution, target engagement evidence in native systems, off-target profiling, and mechanism-of-action mapping. We also help you choose between standard TPP, 2D-TPP profiling, and PISA profiling based on your project goal, sample constraints, and decision stage.

Key Advantages:

Proteome-wide thermal stability readout without compound tagging
Useful for target deconvolution, selectivity review, and mechanism studies
Compatible with cells, lysates, tissues, and challenging protein systems
Integrated bioinformatics that turns thermal shifts into practical decisions

Discuss Your TPP Project View sample requirements

Thermal Proteome Profiling service overview showing proteome-wide target engagement, off-target profiling, and label-free mass spectrometry workflow

What Is TPP Why Use TPP TPP Modes Workflow Technology Comparison Sample Demo Case Study FAQ

What Is Thermal Proteome Profiling (TPP)?

Thermal proteome profiling is a mass-spectrometry-based strategy that links ligand binding to protein thermal stability changes across a temperature series. After samples are heated under matched treated and control conditions, proteins with altered stability remain soluble or precipitate differently, and LC-MS/MS then measures those changes across the proteome.

This is why TPP is so useful for unbiased target discovery, off-target review, and pathway-level interpretation. It gives you a broad view of how a compound affects protein stability in cells, lysates, tissues, and other relevant biological systems.

For projects that need a concentration-dependent thermal stability design, we can also support 2D-TPP profiling. For higher-throughput thermal solubility screening, we can help you assess whether PISA profiling is the better fit.

Why Drug Discovery Teams Use TPP

Phenotypic hit deconvolution

When a compound changes a phenotype but the direct molecular basis is unclear, TPP can generate a ranked list of proteins with significant stability shifts and give you a practical starting point for target nomination.

Off-target profiling

TPP helps reveal proteins whose stability changes outside the intended mechanism, giving you a proteome-wide view of selectivity risk before you move deeper into optimization.

Target engagement in native systems

Compared with purified-protein assays, TPP keeps you closer to the biological context that matters, which is especially helpful for intact cells, native lysates, and membrane-rich systems.

Mechanism-of-action support

Some stability changes point toward direct binding, while others suggest pathway remodeling or protein-complex effects. TPP helps you see both and supports more informed next-step decisions.

What You Can Learn from a TPP Study

With the right design, we can use TPP to help you identify candidate targets behind phenotypic activity, compare analogs at the proteome level, review selectivity and off-target risk, generate target-level melting evidence, and decide when a follow-up workflow such as CETSA-MS, LiP-MS, or dose-response thermal stability analysis is the best next step.

Our TPP Modes and How We Help You Choose

Not every project needs the same TPP format. We help you choose the mode that best matches your scientific question.

MODE 1

Standard Temperature-Range TPP

This is the strongest starting point when you want full thermal profiles and clear target deconvolution logic.

Well suited to phenotypic hit follow-up
Supports proteome-wide target discovery
Useful for first-pass off-target screening

MODE 2

2D-TPP

This design adds concentration as a second dimension and is useful when you need richer compound ranking logic.

Supports analog comparison
Stronger apparent potency-related interpretation
Ideal for projects that need concentration-dependent stability evidence

MODE 3

PISA

PISA is useful when throughput matters more than full curve detail and can be a better fit for broader comparative studies.

Efficient for larger comparison sets
Helpful when material burden needs to be reduced
Useful for earlier-stage expansion work

MODE 4

Orthogonal follow-up planning

After TPP identifies the most relevant proteins, we can help plan the next validation step with complementary workflows.

CETSA-MS for narrower validation
LiP-MS for conformational support
FPOP-MS for structural context

From Sample Intake to Final Result Delivery: Our TPP Workflow

Once your samples enter the project, we move through a complete technical and service workflow. This is the actual experimental path from sample planning to interpretable conclusions.

Study design and feasibility review

We review your biological question, compound class, sample type, matrix complexity, and project goal to decide whether standard TPP, 2D-TPP profiling, or PISA profiling is the best fit.

Sample receipt and QC review

After receipt, we verify sample identity, grouping, handling notes, and replicate structure, then assess whether the material is strong enough for the planned design.

Thermal challenge under matched conditions

We expose treated and untreated samples to a planned temperature series so proteins with altered stability show measurable solubility differences.

Soluble fraction recovery and proteomic preparation

After heating, we recover the relevant fractions, digest proteins to peptides, and prepare them for quantitative LC-MS/MS analysis.

LC-MS/MS acquisition and quantitative analysis

We measure temperature-dependent abundance patterns across thousands of proteins and convert thermal behavior into proteome-wide quantitative evidence.

Curve fitting, interpretation, and final reporting

We model the data across temperatures or concentrations, identify significant shifts, annotate candidate proteins, and deliver a structured report with technical discussion.

Vertical workflow diagram for Thermal Proteome Profiling showing study design, sample QC, thermal challenge, sample preparation, LC-MS/MS, and data interpretation

For related workflows, see:

PISA profiling

Projects We Handle Well

We can support TPP studies across several common discovery scenarios.

Hit deconvolution from phenotypic screens

We use proteome-wide thermal shifts to prioritize proteins most likely linked to compound activity and turn an active phenotype into a tractable target list.

Off-target and safety profiling

When the concern is not only efficacy but also selectivity, TPP gives a broad picture of stability changes across the proteome and helps flag proteins that may require attention before lead advancement.

Challenging targets, including membrane-associated systems

Membrane proteins and native complexes are often difficult to study with classic affinity workflows, so TPP becomes especially attractive when preserving native behavior matters.

Target engagement in relevant models

If you need evidence closer to your efficacy model, we can plan TPP around intact cells, lysates, tissues, or selected complex sample backgrounds.

How TPP Compares with Other Target-Identification Methods

Method	Best For	Main Strength	Main Limitation	When We Usually Recommend It
TPP	Proteome-wide target deconvolution, off-target profiling, mechanism studies	Label-free, broad, native-context friendly	Direct and indirect effects still need interpretation	When you need unbiased proteome-level evidence
CETSA-MS	Focused target engagement review	Easier targeted follow-up	Narrower scope than full TPP	When you already have a short target list
2D-TPP	Compound ranking and concentration-dependent behavior	Stronger potency-related thermal evidence	More complex design	When analog comparison matters
PISA	Higher-throughput thermal screening	Efficient and scalable	Less detailed than full curve-rich TPP	When throughput is the priority
ABPP / pull-down	Direct binder confirmation for suitable chemotypes	Strong direct-binding logic in the right setup	Usually needs probe or tagging strategy	When chemistry allows a modified molecule
SPR / BLI	Purified-target interaction measurement	Clean binding kinetics for defined targets	Not proteome-wide; less native context	When you already know the target and need biophysical binding data
LiP-MS	Conformational and site-level change mapping	Adds structural protection logic	Different readout than thermal stability	When you want orthogonal conformational evidence

Selection Strategy

Choose TPP when the question is broad and discovery-oriented. Choose 2D-TPP profiling when compound ranking matters. Choose PISA profiling when throughput or sample burden is the main concern. Choose CETSA-MS when you need narrower validation on selected targets. Add LiP-MS when you want extra conformational evidence, and use SPR/BLI only after you already know which purified target deserves detailed kinetic work.

Sample Requirements for Common TPP Projects

Sample Type	Recommended Starting Amount	Replicates	Notes
Cultured cells (suspension or adherent)	5×10^6 to 1×10^7 cells	≥3	Strong default starting point for many TPP studies
Trace cell projects	200–5000 cells	≥3	Feasibility review required for low-input designs
Soft tissues	100 mg	≥3	Useful baseline for many tissue-based TPP studies
Hard tissues / difficult solid tissues	200 mg label-free; 300–500 mg preferred	≥3	Helpful when extraction efficiency may be lower
Microbial pellets	50 μL pellet; 100 μL larger-size recommendation	≥3	Wash thoroughly to reduce medium-derived protein contamination
Plasma / serum without depletion	20 μL	≥3	Keep collection tube type and handling consistent
Plasma / serum with depletion	50–100 μL	≥3	Better fit when deeper coverage is needed

Freeze samples immediately after collection when possible, store at -80°C before shipment, and ship on dry ice. Keep biological replicates consistent in collection timing and processing conditions. If your project uses membrane-rich fractions, unusual lysis conditions, or limited material, we review feasibility before launch.

Demo Results You Can Expect from a TPP Project

Volcano plot of proteome-wide thermal stability shifts highlighting significant proteins

Volcano plot of proteome-wide thermal shifts

Melting curves and dose-response thermal stability plots for priority proteins

Melting curves for high-priority proteins

2D thermal stability landscape showing protein response across temperature and concentration

Dose-response or 2D stability landscape

In addition to figure-ready visuals, we provide ranked target tables and functional interpretation so you can see whether the response suggests a narrow target effect or broader biological rewiring.

Case Study: Membrane-Mimetic Thermal Proteome Profiling for Membrane Targets

Membrane-mimetic thermal proteome profiling toward mapping membrane protein–ligand dynamic interactions

Background

Membrane proteins are highly important in drug discovery, but they are difficult to study under conditions that preserve native behavior. This study developed a membrane-mimetic thermal proteome profiling workflow to make membrane-protein target discovery more practical in a proteome-wide setting.

Methods

The researchers combined a membrane-mimetic preparation strategy with thermal proteome profiling to analyze ligand-driven stability changes in membrane proteins. Samples were prepared under conditions designed to preserve membrane-protein behavior, treated with ligand, challenged across temperature conditions, and analyzed by mass spectrometry.

Results

The article's Figure 2 combines SDS-PAGE review, reproducibility assessment, melting-curve evidence, and a volcano-plot view of significant stability changes. The authors showed that the workflow could detect ligand-associated stability responses in membrane-associated proteins and support candidate identification in a difficult target class.

Conclusion

This case shows why TPP is valuable when classic target-identification approaches struggle with membrane proteins or complex sample environments. It also reflects the kind of result structure we aim to deliver: workflow control, proteome-wide screening logic, target-level curve evidence, and decision-ready prioritization.

Representative thermal proteome profiling result image showing significance-based target prioritization

Figure reference: Figure 2 in the linked article includes SDS-PAGE, reproducibility plots, melting evidence, and a volcano-plot view of membrane-protein stability changes.

Bioinformatics Analysis That Turns Thermal Shifts into Decisions

A TPP project is only useful if the output becomes interpretable. That is why we treat bioinformatics as part of the service rather than an afterthought.

Protein-level statistical testing
Candidate ranking based on shift strength and reproducibility
Melting-curve review for priority targets
Concentration-response interpretation where applicable
Pathway and enrichment analysis
Functional clustering of candidate targets
Comparison across compounds, groups, or treatment conditions
Export-ready result tables for internal review

This is how we help move the project from "proteins changed" to "these proteins matter, and here is why they should be validated next."

FAQ

Frequently Asked Questions

Q: What is the difference between TPP and CETSA?

CETSA is usually used in a more targeted way, while TPP expands the same thermal-stability logic to a proteome-wide LC-MS/MS readout. If your question is broad and discovery-driven, TPP is usually the better starting point. If the question is already narrowed to one or a few proteins, CETSA-MS is often the better follow-up tool.

Q: When should I choose 2D-TPP instead of standard TPP?

Choose 2D-TPP profiling when you need stronger concentration-dependent evidence, analog comparison, or clearer compound-ranking logic. Standard TPP is usually the better first step for target deconvolution.

Q: Can you work with cells, lysates, and tissues?

Yes. We can support intact cells, lysates, tissues, and selected complex matrices as long as the project design and material quality are appropriate. Sample amount, matrix complexity, and study goal guide the final setup.

Q: How many replicates should I prepare?

For most TPP projects, we prefer at least three biological replicates per group because this improves reproducibility and interpretation confidence.

Q: How do you handle difficult samples such as membrane-rich systems?

We assess feasibility during scoping and may recommend a modified design or a complementary workflow such as LiP-MS or FPOP-MS if the biological question needs more structural context.

Q: Can TPP separate direct binders from indirect pathway effects?

TPP is very strong for discovery, but interpretation still matters. A stability shift can reflect direct binding, indirect response, or complex remodeling. That is why we combine statistical filtering, curve inspection, annotation, and follow-up planning rather than treating every shifted protein as automatically direct.

References

Plan Your Thermal Proteome Profiling Study with Us

Share your compound, sample type, and project goal with us, and we will help you design a TPP strategy that fits your discovery question and downstream decision path.

Start your inquiry

For Research Use Only. Not for use in diagnostic procedures.

Online Inquiry

Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to for inquiries.