HomeServicesBioinformatics & Multi-Omics AnalysisProteomics & Post-Translational Modification Analysis
Ref H8
Computational Service
Confidence Reported
Scoped After Feasibility Review
Service Overview
Proteomics measures what transcriptomics only implies. We process quantitative mass spectrometry data — label-free, TMT and DIA — from search and quantification through statistical testing to pathway interpretation, and we handle post-translational modification data including phosphorylation, acetylation, ubiquitination, lactylation, succinylation and palmitoylation. Modification analysis is treated as a distinct problem, with site localisation confidence and occupancy normalisation handled explicitly rather than folded into protein-level results.
Key Features & Advantages
Site Localisation Confidence Reported
Modification sites are delivered with localisation probability, so a site placed ambiguously between two adjacent residues is not presented as if it were certain.
Occupancy Separated From Abundance
Modification changes are normalised to protein-level abundance where the data permits, distinguishing genuine regulation from a protein simply being more present.
Missing Values Handled Deliberately
Imputation strategy is chosen for the missingness mechanism and reported, since proteomics conclusions are notoriously sensitive to this choice.
Network-Level Interpretation
Results are mapped onto interaction networks, kinase–substrate relationships and pathways, which converts a protein list into a mechanistic account.
Where This Service Is Used
1Comparing protein abundance between treatment conditions or disease states
2Mapping signalling changes through phosphoproteomic analysis after perturbation
3Identifying interaction partners from pulldown or proximity labelling experiments
4Characterising a drug mechanism of action at the protein level
5Studying emerging modifications such as lactylation in a metabolic or disease context
Methods and Techniques Applied
1Raw data processing, database search and false discovery rate control at peptide and protein level
2Quantification for label-free, isobaric labelling and data-independent acquisition workflows
3Normalisation, batch correction and missing value assessment with a documented imputation strategy
4Differential abundance testing with appropriate models and multiple testing correction
5Modification site identification with localisation scoring and occupancy normalisation
6Functional interpretation: pathway enrichment, kinase–substrate inference and network mapping
What We Need From You
1Raw mass spectrometry files or a search-engine output table, with the acquisition method described
2Sample metadata including group, batch, labelling scheme and any technical replication
3The organism and, where relevant, a preferred sequence database or custom construct sequences
4The biological question and the comparisons that matter
What You Receive
1Protein and peptide identification and quantification tables with quality metrics
2Differential abundance results with statistics and effect sizes
3Modification site tables including localisation probability and occupancy where computable
4Pathway, network and kinase activity inference results
5Publication-quality figures, methods text and reproducible analysis code
What We Compute and Report
1Protein and peptide identifications with false discovery rate control at both levels
2Quantitative abundance matrices with normalisation and batch assessment documented
3Differential abundance statistics with effect sizes and multiple-testing correction
4Modification site tables with localisation probability and occupancy where computable
5Pathway, network and kinase activity inference results
Questions We Are Asked Before Scoping
Can you analyse data from any instrument?
▸Yes for standard vendor formats from the major platforms. Unusual acquisition schemes are assessed during scoping before we commit to a workflow.
Why do protein and mRNA results disagree?
▸Because they measure different things. Post-transcriptional regulation, protein turnover and detection limits all contribute. Disagreement is biologically informative and we interpret it rather than explain it away.
How many replicates are needed?
▸Three biological replicates per group is the practical minimum; four or five provides much better power, particularly for modification analysis where variability is higher.
Interpretation and Limitations
Computational predictions prioritise hypotheses; they do not independently establish binding, biological activity, therapeutic efficacy, safety or clinical validity. Performance depends on input quality, target class, the structural evidence available and the applicability domain of the selected methods. Scores used for ranking are comparative devices and should not be read as measured quantities. All deliverables are for research use only and are not intended for diagnostic or therapeutic use.
Is This the Right Service for You?
Choose this when
Protein-level change must be established rather than inferred from transcripts
Signalling changes after perturbation need mapping at modification-site resolution
Interaction partners from pulldown or proximity labelling need rigorous analysis
Consider another service when
Transcript-level change is sufficient and cheaper
Bulk & Single-Cell RNA-Seq Analysis Small molecule metabolites are the readout
Metabolomics & Mass Spectrometry Analysis What Goes Wrong, and How We Handle It
These are the failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.
Modification changes reported without correcting for protein abundance
Occupancy is normalised to protein level where the data allows, separating regulation from a protein simply being more abundant.
Imputation choices silently driving the conclusions
Missingness is characterised and the imputation strategy is documented, because proteomics results are notoriously sensitive to it.
Ambiguous site localisation presented as definite
Localisation probability is reported per site, so a modification placed between two adjacent residues is visible as such.
A Worked Example
Separating signalling from expression after inhibitor treatment
The situation
Phosphosite intensities dropped sharply after treatment and the team attributed it to pathway inhibition.
What the work involved
Protein-level abundance was quantified in parallel, occupancy was normalised against it, and kinase activity was inferred from the corrected site-level changes.
What came back
Roughly a third of the apparent signalling changes tracked protein degradation rather than reduced phosphorylation. The corrected set produced a cleaner and different kinase activity profile.
Illustrative of the shape this work takes. Details are generalised, no client or target is identified, and scope and outcome vary with the system in question.
Service Workflow
1
Scientific Consultation
We discuss the objective, the decision it supports and the data you hold. Nothing is quoted before we understand what the result has to answer.
2
Feasibility Review
We check that the data, target class and available structural evidence can support the proposed approach, and say plainly where they cannot.
3
Technical Proposal
Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.
4
Computation and QC
The analysis runs on pinned tool versions in a containerised environment, with quality checkpoints and method comparison where that is informative.
5
Report and Follow-Up
You receive the ranked results, the documented methods, the limitations and a proposed validation plan, plus support in interpreting them.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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4
Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day