What Is PTM Proteomics?
Post-translational modifications (PTMs) are covalent chemical alterations to amino acid residues that occur after protein synthesis, dramatically expanding the functional diversity of the proteome. More than 400 distinct PTM types have been described in eukaryotes — from the well-characterized (phosphorylation, glycosylation, ubiquitylation, acetylation, methylation) to recently discovered metabolic marks (lactylation, crotonylation, succinylation) and redox-sensitive cysteine modifications that respond dynamically to cellular redox state.
PTMs regulate virtually every aspect of protein function: enzymatic activity, protein-protein interactions, subcellular localization, stability, and turnover. Disruption of PTM patterns — through mutations in modification enzymes, aberrant kinase activity, or altered ubiquitin pathway function — is a hallmark of cancer, neurodegeneration, metabolic disease, and immune dysfunction. Mass spectrometry-based PTM proteomics is the definitive technology for identifying modification sites, quantifying their abundance, and connecting PTM changes to biological function — providing the site-level resolution and proteome-wide coverage that antibody-based assays and activity measurements cannot deliver.
Our PTM proteomics platform integrates three capabilities that define project quality: enrichment chemistry (modification-specific capture of low-abundance modified peptides from a complex background), high-resolution MS acquisition (Orbitrap Fusion Lumos, Q Exactive HF-X, timsTOF Pro — matched to each modification type), and PTM-specific bioinformatics (site localization, occupancy calculation, pathway-level signaling interpretation). Every project is delivered with raw data, identification and quantification tables, statistical results, and publication-ready figures.
Our PTM Proteomics Services
Our service portfolio is organized across six areas — from technology-level discovery and quantification tools to modification-type-specific profiling platforms. Each links to a dedicated service page with full details on enrichment protocols, sample requirements, instrument platforms, and deliverables.
PTM Discovery Services
Unbiased, proteome-scale identification of modification sites — without requiring prior knowledge of which proteins are modified or which modifications are present.
Proteome-wide identification of all detectable PTMs simultaneously across the full modification landscape of a sample — delivering a systems-level PTM inventory with site localization, protein annotation, co-modification analysis, and pathway-level context without prior enrichment bias.
Unbiased detection of known and unanticipated PTMs using open mass-shift database searching — identifying modifications without predefined variable modification lists. Optimal for novel modification discovery in unstudied organisms, disease states, or drug-treated samples where the modification repertoire is unknown.
High-confidence assignment of modification positions with site localization probability scoring (phosphoRS, ptmRS, AScore) — distinguishing confidently assigned sites from ambiguous candidates and providing residue-level precision required for downstream functional validation and structural studies.
Sequential multi-modification enrichment from the same protein digest — generating site-level data for two or more PTM types simultaneously. Enables crosstalk analysis between modification types and construction of multi-layer regulatory networks within a single project.
Characterization of intact protein proteoforms — species carrying distinct combinations of modifications at defined sites — using top-down or middle-down MS approaches. Resolves the combinatorial modification complexity that peptide-level bottom-up workflows cannot capture.
PTM Quantification Services
Relative and absolute quantification of modification site occupancy between conditions — from high-throughput multiplexed comparisons to single-site stoichiometry. View full PTM Quantification hub →
Data-independent acquisition for high-reproducibility, low-missing-value PTM quantification across large cohorts. Recommended for biomarker discovery studies and projects requiring quantitative completeness across many samples — typically 10+ conditions or time points.
Isobaric multiplexed PTM quantification — up to 16 conditions in a single LC-MS/MS run with high throughput and minimal batch effects. Optimal for time-course experiments, dose-response studies, and multi-group comparative analyses requiring deep modification coverage.
Metabolic stable isotope labeling delivering the lowest ratio noise for two-condition PTM comparisons in dividing cell lines — the gold standard for phosphoproteomic drug MoA studies and head-to-head site-level fold-change measurement.
Targeted parallel reaction monitoring for site-specific, high-sensitivity PTM quantification in validation studies — confirming discovery-phase findings at defined modification sites with optimized sensitivity, selectivity, and defined LOD/LOQ.
Stable-isotope dilution MS for absolute molar quantification of modified peptides — providing site occupancy stoichiometry, copy number per cell, and calibration-curve-based concentration values (fmol/μg protein) for defined modification sites.
Quantification of the fraction of a protein population carrying a modification at a defined site — measuring stoichiometry rather than raw intensity. Essential for understanding regulatory switching at any modification type and for comparing occupancy across treatment conditions.
Core PTM Type Services
Modification-specific enrichment and LC-MS/MS profiling services for all major PTM categories — each with dedicated protocols optimized for enrichment efficiency, site localization, and quantitative accuracy.
Global Ser/Thr/Tyr phosphorylation profiling by IMAC or TiO2 enrichment — identifying 10,000–50,000+ phosphosites per project with kinase-substrate network inference (KSEA) and signaling pathway annotation. The core technology for kinase inhibitor MoA studies and signaling pathway research.
Comprehensive N- and O-glycosylation profiling covering glycosite identification, intact glycopeptide analysis, glycan structure characterization, and quantitative glycoproteomics — applicable to cells, tissues, biofluids, recombinant proteins, and biopharmaceuticals.
Proteome-wide ubiquitination site mapping via diGLY (K-ε-GG) antibody immunoaffinity enrichment — identifying thousands of ubiquitinated lysines and quantifying substrate dynamics under proteasome inhibition, E3 ligase perturbation, or targeted protein degrader treatment.
Pan-acetyllysine and N-terminal acetylation profiling using antibody-based enrichment — covering histone epigenetic marks, metabolic enzyme regulation, and protein stability control, with quantitative stoichiometry measurement across experimental conditions.
Dedicated histone modification profiling using acid extraction, chemical derivatization, and optimized LC-MS/MS protocols — mapping H3, H4, H2A, and H2B modification marks including methylation, acetylation, phosphorylation, and ubiquitination with combinatorial co-occurrence analysis.
Detection of mono-, di-, and tri-methylation at lysine and arginine residues using antibody enrichment or heavy methyl-SILAC — covering chromatin biology, RNA-binding protein regulation, and protein-protein interaction modulation via methyl-reader domain recognition.
SUMO-modified protein identification and site mapping using SUMO-tagged expression systems or motif antibody enrichment — covering nuclear transport, DNA damage response, and transcription factor regulation with quantitative comparison across conditions.
Site-specific detection of palmitoylation, myristoylation, prenylation, and GPI anchoring using acyl-RAC, ABE, or metabolic labeling — essential for membrane protein biology, Ras signaling, and lipid-regulated protein trafficking research.
Quantitative proteome-wide mapping of cysteine redox states — reduced, oxidized, sulfenic acid, S-glutathionylated, S-nitrosylated — using differential alkylation strategies. Includes Reactive Cysteine Profiling for covalent drug target discovery.
Emerging & Metabolic PTM Services
Novel lysine acylation marks discovered over the past decade as key regulators of cellular metabolism, epigenetic programming, and disease — each with dedicated enrichment and quantitative profiling workflows.
Quantitative profiling of L-lactylation — a Warburg effect-linked modification connecting glycolytic metabolism to epigenetic regulation on histone and non-histone proteins. Detected by anti-lactyllysine antibody enrichment with MS/MS validation of modification sites.
Site-resolved mapping of lysine crotonylation — an active transcription-associated epigenetic acyl mark found on histones and regulatory proteins. Anti-crotonyllysine antibody enrichment combined with Orbitrap or timsTOF detection for high-confidence site assignment.
Proteome-wide succinylation profiling using anti-succinyllysine antibody enrichment — with applications in mitochondrial metabolism, TCA cycle enzyme regulation, and SIRT5 desuccinylase substrate discovery.
Quantitative profiling of multiple short-chain acyl modifications in parallel — covering propionylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation, and additional acyl marks in a coordinated multi-enrichment workflow.
O-GlcNAcylation profiling on serine and threonine residues — a nutrient-sensing modification at the interface of glycolysis and transcriptional regulation. Site mapping and quantification across conditions using chemoenzymatic labeling or lectins coupled to LC-MS/MS.
Technology & Enrichment Platform
Strategy overview covering bottom-up, middle-down, and top-down acquisition modes — with guidance on matching the right MS approach to modification type, protein size, and required site localization resolution. Includes instrument platform selection for each PTM class.
How Our PTM Proteomics Service Works
Step 1: Sample Submission & Project Design
Submit your sample type, modification of interest, experimental design (number of conditions, replicates), and scientific question. Our team recommends the optimal enrichment strategy, quantification workflow, and instrument platform — and provides confirmed sample requirements, input amounts, and pre-collection handling protocols before you ship.
Accepted sample types: cultured cells, fresh/frozen tissue, FFPE sections, plasma, serum, urine, CSF, exosome pellets, recombinant proteins, pre-extracted lysates.
Step 2: Sample Preparation & PTM Enrichment
Proteins are extracted, denatured, reduced, alkylated, and digested with trypsin using protocols validated for each sample matrix. Modification-specific enrichment is applied — IMAC/TiO2 for phosphopeptides, diGLY antibody IP for ubiquitination, HILIC or lectin affinity for glycopeptides, pan-acyl-lysine antibody for acetylation/acylation marks, acyl-RAC for palmitoylation, differential alkylation for redox cysteines, and acid extraction plus derivatization for histone modifications. Enrichment efficiency is monitored by internal spike-in controls.
Step 3: LC-MS/MS Acquisition
Enriched peptides are analyzed by nanoflow UHPLC coupled to high-resolution mass spectrometry. Platform selection is matched to the modification: Orbitrap Fusion Lumos with EThcD fragmentation for labile modifications and site localization; Q Exactive HF-X for high-throughput phospho and ubiquitin profiling; Bruker timsTOF Pro for ion-mobility-enhanced 4D-DIA PTM quantification. Instrument QC includes mass accuracy monitoring, iRT standard injection, and spray stability validation before each run.
Step 4: Data Analysis & Site Localization
Raw data are processed using MaxQuant, Proteome Discoverer, or Spectronaut with modification-specific variable modifications, 1% FDR at peptide and protein level, and ptmRS/phosphoRS site localization scoring. Quantitative matrices are generated with normalized site-level intensities or ratios. Statistical analysis includes t-test or limma for differential site regulation, with Benjamini-Hochberg FDR correction and volcano plot visualization.
Step 5: Biological Interpretation & Reporting
Regulated modification sites are mapped to kinase-substrate databases (KSEA for phospho), E3 ligase substrate networks (ubiquitin), or functional annotation databases. GO, KEGG, and Reactome pathway enrichment analysis is performed on proteins with significantly regulated modification sites. Deliverables include raw data files, identification and quantification tables, statistical results, bioinformatics figures, and a project report with publication-ready methods text and key findings summary.
Why Choose Creative Proteomics for PTM Analysis
✅ Broadest PTM Coverage
We maintain validated enrichment and detection protocols for 100+ modification types — from high-volume services (phosphoproteomics, glycoproteomics, ubiquitylomics) to specialized emerging marks (lactylation, crotonylation, redox cysteines) and rare modifications. One CRO covers your entire PTM research program, with no need to coordinate multiple vendors across modification types.
✅ Dedicated PTM Instrumentation
Our instrument suite is configured specifically for PTM analysis: Thermo Orbitrap Fusion Lumos with EThcD fragmentation for labile modification site localization and O-glycopeptide characterization; Q Exactive HF-X for deep-coverage phospho and ubiquitin profiling; Bruker timsTOF Pro for 4D-DIA PTM quantification with ion mobility separation — each matched to the modification class and workflow requirements of your project.
✅ Validated Enrichment Chemistry
Every enrichment protocol in our platform has been independently validated for enrichment specificity, recovery, and reproducibility before deployment in client projects. We monitor enrichment efficiency per batch using spike-in standards and report enrichment QC metrics alongside each dataset — so you know the quality of the enrichment, not just the depth of the database search.
✅ Full-Pipeline PTM Bioinformatics
Our bioinformatics output goes beyond a modification site list: site localization probability scores, occupancy stoichiometry calculations, kinase activity inference (KSEA), PTM crosstalk network analysis, motif enrichment, GO/KEGG/Reactome pathway annotation, and integrated multi-PTM correlation analysis are all delivered as standard components of the project report — not add-on services requiring extra negotiation.
✅ Discovery-to-Validation in One Team
Our platform supports the full PTM research lifecycle without handoffs between vendors: global discovery (open-search, global profiling) → site identification → quantitative profiling (DIA, TMT, SILAC) → targeted validation (PRM) → absolute quantification (stable isotope dilution). Projects designed to span multiple phases benefit from consistent protocols, sample management, and bioinformatics across every stage.
✅ Sample Collection Support
Many PTM experiments fail at the sample collection stage — phosphatases active in lysates, DUBs removing ubiquitin chains, redox states equilibrating before fixation. We provide modification-specific sample handling guides (NEM for ubiquitin, phosphatase inhibitors for phospho, trapping reagents for redox PTMs) and pre-project consultation to ensure your samples arrive with intact modification states regardless of collection site or biological model.
FAQs
Which PTM quantification strategy should I choose — DIA, TMT, SILAC, or label-free?
The choice depends on sample type, number of conditions, and required quantitative performance. DIA/SWATH is our default recommendation for large cohorts (10+ samples per condition) or any study where quantitative completeness across many samples is essential — it produces the lowest missing-value rates and scales well for biomarker discovery pipelines. TMT multiplexing (up to 16-plex) is preferred for high-throughput multi-condition comparisons within a single instrument run, minimizing batch effects and maximizing throughput for time-course or dose-response experiments. SILAC delivers the lowest ratio noise for two-condition head-to-head comparisons in dividing cell lines and is the benchmark for phosphoproteomic drug MoA studies. Label-free quantification is the most flexible option — applicable to any sample type including primary cells, tissue, and biofluids where metabolic or chemical labeling is not feasible. We provide a workflow recommendation with specific performance expectations for your experimental design when you submit a project inquiry.
How many modification sites can I expect to identify in my samples?
Coverage depends heavily on modification type, sample matrix, input amount, and whether offline fractionation is applied. For phosphoproteomics from cell lines (≥5 × 106 cells) using IMAC enrichment with single-shot acquisition, we typically identify 10,000–20,000 phosphosites; with high-pH offline fractionation, this extends to 30,000–50,000+ sites. For ubiquitinomics (diGLY) from ≥10 mg total protein, 5,000–15,000 K-ε-GG sites are typical. For acetylomics from ≥3 mg protein, 5,000–10,000 acetylation sites. For glycoproteomics, coverage varies by matrix and enrichment strategy. Tissue and biofluid samples typically yield lower coverage than cultured cell lines due to sample complexity and protein composition. We provide modification-specific coverage estimates for your sample type at project initiation.
Can you profile multiple PTM types from the same sample simultaneously?
Yes — our Pan PTM Proteomics and Multi-PTM Crosstalk Profiling services apply sequential modification-specific enrichment workflows to the same protein digest. Common and validated combinations include: phospho + ubiquitin (diGLY) for phosphodegron-driven degradation studies; phospho + acetyl for chromatin regulation; acyl mark panels (acetyl + crotonyl + succinyl + lactyl) for metabolic epigenetics research; and glyco + phospho for glycoprotein signaling studies. The feasibility of a specific combination depends on input requirements for each enrichment step and the compatibility of the enrichment chemistries involved. We confirm the optimal multi-PTM design and required input amounts during project consultation.
What sample preparation steps must I complete before shipping?
Pre-collection requirements vary critically by modification type. For phosphoproteomics: add phosphatase inhibitor cocktail (PhosSTOP or NaF + Na₃VO₄) to lysis buffer immediately before use; lyse on ice. For ubiquitinomics: add 20 mM NEM (N-ethylmaleimide) to lysis buffer to block deubiquitinases — this is the single most important step and must be done at lysis, not afterward. For redox/cysteine PTMs: add the modification-appropriate trapping reagent (iodoacetamide, NEM, or sodium arsenite) immediately at lysis before any oxidation can occur. For histone modification analysis: snap-freeze cell pellets within 60 seconds of media removal; do not allow cells to remain at room temperature after harvest. We provide a modification-specific sample collection guide for every project type — please request this before sample collection to ensure modification states are preserved from biological sample to our laboratory.
What bioinformatics deliverables are included in a standard PTM project?
Every PTM project includes: raw LC-MS/MS data files in vendor format; modified peptide identification table with sequence, modified residue, localization probability score, charge state, and FDR; normalized site-level quantification matrix; differential regulation results (log2 fold-change, p-value, adjusted p-value) with volcano plot; hierarchical clustering heatmap of significantly regulated sites; GO biological process, molecular function, and KEGG pathway enrichment analysis on proteins with regulated modification sites; and a project report with key findings and a publication-ready methods section. For phosphoproteomics, kinase-substrate enrichment analysis (KSEA) and signaling network visualization are included as standard. For ubiquitinomics, E3 ligase substrate network annotation is included. Additional custom analyses — PTM crosstalk, site motif analysis, cross-dataset integration — are available upon request.
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