Discover and compare proteins
Use broad identification and quantitative comparison to find proteins and pathways associated with a treatment, phenotype or disease state.
Discovery Proteomics
NGPro™ by Creative Proteomics
Proteomics CRO Services for Discovery, Quantification and Targeted Validation
Build a mass spectrometry workflow around the decision your program needs to make. Creative Proteomics provides discovery proteomics, DIA quantitative proteomics, 4D proteomics, phosphoproteomics, immunopeptidomics and targeted verification—from feasibility assessment through data interpretation.
Popular Proteomics Services
- Study-specific workflow design
- Pilot-to-scale planning
- Defined data deliverables
Project Decision MapQUESTION → DATA
01
Define the biological question
Discovery, cohort comparison, signaling, antigen presentation or target verification.
02
Assess the sample
Matrix, amount, cohort size, groups, preparation needs and technical constraints.
03
Select the acquisition strategy
DDA, DIA, ion-mobility-enabled 4D, enrichment, PRM or SRM/MRM.
04
Define decision-ready outputs
Quantification, statistics, pathways, figures, raw data and targeted follow-up.
Find by sample type
Start with the research objective
Choose a Proteomics Service by Research Objective
Start with the decision your study needs to support: discover regulated proteins, quantify a cohort, resolve a difficult sample, study signaling or verify a shortlist. Creative Proteomics will match that objective with an appropriate proteomics workflow.
Identify proteins at scale
Characterize complex samples when broad protein identification is the primary objective and quantitative comparison is not the only endpoint.
Large-Scale Protein IdentificationQuantify larger cohorts
Use data-independent acquisition when consistent peptide and protein quantification across multiple samples is central to the study.
DIA Quantitative ProteomicsResolve limited or complex samples
Add ion mobility when sample amount, matrix complexity or the desired depth makes another separation dimension valuable.
4D ProteomicsStudy signaling and regulation
Enrich and profile phosphorylation or other post-translational modifications to investigate regulatory changes beyond total protein abundance.
PhosphoproteomicsProfile presented peptides
Characterize MHC-associated peptides for antigen presentation, neoantigen research and immunology programs.
ImmunopeptidomicsVerify selected targets
Move from a discovery shortlist to focused peptide or protein measurement with PRM, SRM/MRM or combined DIA-to-PRM strategies.
Targeted ProteomicsMethod selector
Compare Discovery, DIA, 4D and Targeted Proteomics
A method should be selected after the biological objective, sample constraints and required output are clear. The table below provides a practical starting point for project discussions.
| Primary need | Recommended starting point | Best suited to | Next step |
|---|---|---|---|
| Broad protein discovery | Discovery proteomics | Protein identification, differential comparison and pathway generation when targets are not predefined. | Explore DPro |
| Large-scale protein identification | Qualitative discovery workflow | Complex samples where broad protein identification and characterization are the primary objectives. | Explore Protein ID |
| Consistent cohort quantification | DIA quantitative proteomics | Multi-sample studies that prioritize quantitative completeness and comparability. | Explore DIA |
| Low-input or complex material | 4D-DIA or 4D label-free | Studies where ion mobility can improve separation for demanding sample conditions. | Explore 4D-DIA |
| Protein regulation and signaling | Phosphoproteomics or PTM profiling | Kinase signaling, treatment response and modification-site analysis. | Explore PTMs |
| Presented antigen discovery | Immunopeptidomics | MHC-I or MHC-II peptide profiling and neoantigen-oriented research. | Explore Immunopeptidomics |
| Shortlist verification | PRM or SRM/MRM | Focused relative or absolute measurement of predefined proteins or peptides. | Explore PRM |
Where 4D fits:4D proteomics is positioned as a solution for sample and separation challenges—not as the default answer to every proteomics question.
Inputs and outputs
Supported Sample Types and Project Deliverables
Sample suitability and deliverables are confirmed during technical review. This avoids selecting a method before the matrix, available input and downstream use of the data are understood.
Common sample categories
Creative Proteomics can assess diverse biological matrices for proteomics analysis. Difficult or limited samples may require a feasibility review before the main study.
Configurable project deliverables
Outputs are defined in the project scope so the dataset can support the intended research or development decision.
- Study design and method summary
- Sample and acquisition quality-control results
- Protein and peptide identification or quantification tables
- Differential analysis and multivariate statistics
- Functional annotation and pathway enrichment
- Publication-ready figures and analysis files
- Raw data and parameter files as scoped
- Candidate list for targeted follow-up
Program support
Program Support from Pilot Study to Scale
For biotechnology, pharmaceutical and research organizations, Creative Proteomics defines each study around its decision points, sample flow, quality-control checkpoints, analysis outputs and follow-up options.
- Scientific scope review
- Pilot study design
- Sample and metadata plan
- QC checkpoint definition
- Analysis specification
- Phased project planning
- Raw-data requirements
- Targeted follow-up path
From initial question to program decision
PHASE 01
Feasibility and scope
Review the biological objective, matrix, available amount, sample number, groups and required endpoint.
PHASE 02
Pilot and method confirmation
Assess preparation, measurable depth, quality indicators and analysis settings before scaling.
PHASE 03
Scaled execution
Apply the agreed workflow, sample sequence, QC logic and reporting structure to the main cohort.
PHASE 04
Interpretation and follow-up
Connect quantitative results to pathways, candidate prioritization and targeted verification options.
Project workflow
From Sample Preparation to Data Analysis
The exact protocol is study-specific, but every project should make the same five decisions visible: scope, preparation, acquisition, quality review and interpretation.
Study definition
Question, groups, sample number, matrix, input and outputs.
Sample preparation
Extraction, digestion, cleanup, fractionation or enrichment as required.
Mass spectrometry
DDA, DIA, 4D, PTM enrichment or targeted acquisition.
Quality control
Check sample, run and dataset-level quality indicators.
Bioinformatics
Statistics, functional context, figures and candidate prioritization.
Research applications
Proteomics for Drug and Translational Research
Method selection should follow the research phase and the evidence required—from early mechanism work to biomarker prioritization and targeted verification.
DRUG R&D
Mechanism and response
Compare treatment groups, map affected pathways and generate protein candidates associated with pharmacology or toxicity.
Explore the solution → TRANSLATIONALBiomarker discovery
Profile tissues or biofluids, evaluate group differences and prioritize candidates for follow-up measurement.
Explore the solution → IMMUNOLOGYAntigen presentation
Investigate MHC-associated peptides and connect immunopeptidomic findings with therapeutic research questions.
Explore the solution → BIOPROCESSProcess understanding
Use proteomic profiles to compare cell states, process conditions or host-cell-related protein patterns.
Explore the solution →
Research relationships
Great Minds Choose Creative Proteomics
Creative Proteomics supports proteomics projects for research teams across academic medicine, healthcare and biotechnology.
500+Proteomics Projects DeliveredAcross discovery, DIA, 4D and targeted proteomics workflows.
50+Countries & Territories ServedGlobal support for academic and industry research teams.
10+ YearsMulti-Omics ExperienceMass spectrometry and bioinformatics support for research programs.
Institutional names and trademarks are the property of their respective owners.
Frequently asked questions
Proteomics Service FAQs
These are the practical questions that determine method fit, scope, timing and deliverables. A technical discussion can then focus on the details unique to your study.
Prepare a Project InquiryWhich proteomics service should I choose?
Choose discovery proteomics for broad protein identification and group comparison, DIA for consistent quantification across larger cohorts, 4D proteomics when ion mobility can help with limited or complex samples, and PRM or SRM/MRM when specific proteins or peptides must be verified.
What is the difference between DIA and 4D-DIA proteomics?
DIA is a data-independent acquisition strategy for reproducible peptide and protein quantification. 4D-DIA adds ion mobility separation, providing an additional separation dimension that can be useful for complex matrices, low-input material or deeper profiling objectives.
Can a proteomics program begin with a pilot study?
Yes. A pilot can be scoped to assess sample preparation, measurable proteome depth, data quality and analysis settings before a larger project is launched.
What information is needed to scope a proteomics project?
Provide the biological question, sample type, sample number, available amount, study groups, target proteins if applicable, preferred outputs and desired decision timeline. The workflow can then be matched to the study objective.
What data can be included in the project deliverables?
Deliverables can include a study and method summary, quality-control results, protein and peptide identification or quantification tables, statistical comparisons, functional enrichment outputs, figures, and raw data or parameter files as defined in the project scope.
How is project turnaround determined?
The timeline is confirmed after scope review. It depends on sample number, sample preparation, fractionation or enrichment, acquisition strategy, data-analysis depth and any targeted follow-up work.
Plan Your Project with Creative Proteomics
Share your sample type, sample number, study groups, available amount and desired output. The technical team can recommend a starting workflow for your project.
Request a Project Consultation For biotechnology, pharmaceutical and research organizations
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