Endogenous Co-IP-MS
Choose this workflow when You want to enrich a native bait protein using an IP-compatible antibody and identify co-enriched proteins by LC-MS/MS.
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Protein Interaction Analysis Service
Co-IP-MS Protein Interaction Analysis Service
LC-MS/MS-based Co-IP-MS workflows for identifying proteins associated with a target bait, comparing interaction profiles across biological conditions, and prioritizing candidates for follow-up validation.
Use this service when your project has a known bait protein, antibody or tag-based enrichment route, and a need to move from a single interaction question toward a broader, background-aware candidate interactor profile.
- Discover candidate interactors around an endogenous or tagged bait protein.
- Compare bait-associated proteins across treatment, mutation, stimulation, or control groups.
- Filter background proteins using matched controls and prioritize candidates for downstream validation.
Co-IP-MSBait-Centered DiscoveryEndogenous or Tagged BaitCondition ComparisonPilot Available
Research experience
Supporting interaction proteomics projects for academic and industry research groups
Researchers from leading academic and industry organizations have worked with MtoZ Biolabs on protein interaction and LC-MS/MS-based interaction proteomics projects. Project scope, workflow, and controls are tailored to each study.
When This Service Is a Good Fit
Designed for projects where a target protein is already known and the goal is to identify, compare, or prioritize proteins that co-enrich with that bait under defined experimental conditions.
Known bait, unknown partners
You have a target protein and need a ranked list of candidate associated proteins from cells, tissue, or another biological model.
Endogenous interaction discovery
You want to study a native bait protein using an IP-compatible antibody and LC-MS/MS-based interactor identification.
Tagged bait or engineered model
You have a tag-based enrichment system and need mass spectrometry to identify co-purified proteins beyond western blot readouts.
Treatment-dependent changes
You want to compare bait-associated proteins across treatment, stimulation, mutation, time-course, or control groups.
Complex component discovery
You need candidate subunits, regulators, accessory proteins, or complex-associated proteins for downstream validation.
Background-aware candidate filtering
You need controls and data interpretation to separate likely bait-associated proteins from antibody, bead, or sample background.
Choose the Right Co-IP-MS Workflow
Choose a setup based on your bait source, enrichment route, controls, and whether your goal is discovery, comparison, or feasibility evaluation.
Not sure which route fits? Choose Not sure — recommend a workflow in the quote form and share your target, sample type, antibody or tag information, and expected result.
Tagged Bait IP-MS
Choose this workflow when You have HA, Myc, GFP, His, or another tag-based bait system and need interactor discovery or comparison.
Click to preview →Comparative Co-IP-MS
Choose this workflow when You want to compare how mutation, stimulation, inhibitor treatment, stress, or time point changes bait-associated proteins.
Click to preview →Background-Controlled Enrichment Review
Choose this workflow when You need to distinguish bait-associated proteins from antibody, bead, or sample background before full-scale Co-IP-MS analysis.
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Workflow preview
Select a workflow above
After you select a workflow, this panel will summarize the best next step and carry that choice into the quote form.
Service Workflow
A simplified path from project review and enrichment planning to Co-IP, LC-MS/MS acquisition, data analysis, and interpretation-ready reporting.
Project Review
Confirm bait, model, controls, and expected result.
Enrichment Planning
Review antibody, tag, beads, sample input, and controls.
Co-IP Enrichment
Enrich bait-associated proteins with matched controls.
Protein Processing
Digest enriched proteins and prepare peptides for MS.
LC-MS/MS
Acquire peptide data using a matched proteomics workflow.
Report
Deliver candidate tables, QC, comparison, and guidance.
The workflow is adapted to sample type, antibody or tag performance, target abundance, control design, and desired confidence level.
What to Send Us — By Workflow
Use the checklist below to prepare sample type, input amount, and matched controls for the selected Co-IP-MS workflow.
| Workflow | Sample Type | Sample Amount |
|---|---|---|
| Endogenous Co-IP-MS | Cells, tissue, or prepared lysate containing the endogenous bait protein. | ≥1×10⁷ cells, 100-150 μl cell pellet or ≥50 mg tissue. |
| Tagged Bait IP-MS | Cells, tissue, or prepared lysate expressing the tagged bait protein; tagged construct information if applicable. | ≥1×10⁷ cells, 100-150 μl cell pellet or ≥50 mg tissue. |
| Comparative Co-IP-MS | Matched sample groups, such as treatment/control, mutant/wild type, stimulation/time-course, or disease model/control. | At least 1 mg total protein per sample; 2–5 mg preferred. Keep input amount consistent across groups; ≥3 replicates recommended. |
| Background-Controlled Enrichment Review | Test IP sample with appropriate control IPs, such as IgG IP, mock IP, or tag-only IP. | Prepare controls with comparable input when feasible; submit available material for feasibility review. |
Limited sample?
Send the amount you have. Final input is reviewed based on target abundance, enrichment efficiency, background level, and required detection depth.
Results & Deliverables
Deliverables are tailored to the selected Co-IP-MS setup, control design, and comparison goal.
Candidate interactor table
Protein IDs, names, intensity or spectral metrics, enrichment patterns.
Background-aware filtering
Review against IgG, beads-only, tag-only, input, or matched negative controls where included in the design.
Group comparison results
Relative differences across treatment, control, time-course, mutant, or stimulation groups when the study design supports comparison.
QC summary
Sample processing notes, LC-MS/MS acquisition summary, identification metrics, replicate assessment,.
Figures and report
Visual summaries and interpretation notes for candidate prioritization and follow-up experiment planning.
Raw and processed files
Data files and processed result tables can be provided according to project scope and reporting needs.
Platform & Capabilities
Integrated project design, Co-IP enrichment review, LC-MS/MS instrumentation, and QC support for protein interaction discovery.
Project Support
Start Project Review
From enrichment strategy to candidate interpretation
Each project is reviewed around the bait, sample state, antibody or tag route, controls, and expected evidence level.
Workflow recommendation
Endogenous Co-IP-MS, tagged bait IP-MS, comparative Co-IP-MS, or pilot evaluation.
Enrichment review
Antibody, tag, beads, input, elution, and negative control planning.
QC checkpoints
Sample handling, enrichment background, LC-MS/MS performance, and replicate behavior.
Result guidance
Candidate prioritization, confidence factors, and follow-up validation suggestions.
Platform & Software
LC-MS/MS platform
UltiMate3000 RSLCnano Orbitrap Fusion™ Lumos™ Tribrid™
High-sensitivity LC-MS/MS for in-depth proteomics analysis.
Vanquish Neo Orbitrap Fusion™ Lumos™ Tribrid™
Flexible LC-MS/MS acquisition for complex proteomics workflows.
Vanquish Neo Orbitrap Exploris 480
High-resolution LC-MS/MS with robust quantitative performance.
Vanquish Neo astral
High-throughput LC-MS/MS with deep proteome coverage.
Control-aware filteringReplicate reviewCoverage assessmentReport-ready tables
Result Considerations
A brief guide to what Co-IP-MS results can support, what they cannot confirm alone, and which factors affect confidence.
What results can support
Candidate protein associations, bait-centered enrichment patterns, and condition-related interaction changes.
What needs validation
Direct binding, functional relevance, and mechanism usually require reciprocal IP, targeted assays, or functional experiments.
What affects confidence
Target abundance, antibody performance, sample input, background level, controls, replicates, and MS coverage.
Co-IP-MS vs Standard Co-IP / WB
A quick guide to when LC-MS/MS adds value beyond testing one or a few expected interaction partners.
| Scenario | Standard Co-IP / WB | Co-IP-MS |
|---|---|---|
| Known interaction check | Often suitable for testing selected proteins | Can include known proteins but is broader than a single-target readout |
| Unknown partner discovery | Limited by antibody targets selected in advance | Identifies many candidate co-enriched proteins in one experiment |
| Condition comparison | Usually focused on predefined proteins | Can compare broader bait-associated protein profiles across groups |
| Interpretation | Supports selected co-enrichment evidence | Supports candidate association evidence with control-aware prioritization |
FAQs
Frequently asked questions about Co-IP-MS Protein Interaction Analysis Service.
The main output is a list of proteins co-enriched with the bait, supported by LC-MS/MS identification metrics, control-aware filtering, and project-specific result interpretation.
Co-IP-MS provides candidate association evidence. Direct binding, functional relevance, and mechanism usually require follow-up validation such as reciprocal IP, targeted MS, purified-protein assays, or functional experiments.
Common controls include IgG, beads-only, tag-only, input, untransfected or control cell line, untreated control, and matched biological controls depending on the project design.
Yes. Comparative Co-IP-MS can be designed for treatment-control, mutant-wild type, stimulation, inhibitor, time-course, or other matched groups when sample handling and replicates are appropriate.
A pilot is recommended for low-abundance bait proteins, complex tissues, limited sample input, unvalidated antibodies, membrane-associated targets, or projects with high expected background.