Plant Protein Identification
Choose this workflow when You need to identify proteins in plant tissues, organelles, enriched samples, fractions, or gel bands.
Click to preview →
Proteomics Service
Plant Proteomics Service
LC-MS/MS-based plant proteomics for plant protein identification, quantitative proteomics, post-translational modification analysis, and protein interaction analysis across diverse tissues and experimental models.
- Advanced Orbitrap Exploris 480, timsTOF Pro, and Orbitrap Astral platforms support diverse studies.
- Integrated plant metabolomics strengthens pathway and phenotype interpretation.
- Pilot studies assess sample suitability and project feasibility.
Research experience
Supporting plant proteomics projects for academic and industry research groups
Researchers from leading academic and industry organizations have worked with MtoZ Biolabs on plant proteomics projects. Project scope, workflow, and controls are tailored to each study.
When Plant Proteomics Is a Good Fit
Analyze Plant Tissues and Fractions
Help profile proteins in tissues, cells, organelles, membranes, and other plant samples.
Compare Conditions and Stress Responses
Reveal proteome changes across genotypes, treatments, stages, tissues, or time points.
Characterize PTMs and Signaling
Analyze phosphorylation, acetylation, glycosylation, ubiquitination, and other supported PTMs.
Identify Protein Complexes and Interactors
Discover proteins associated with baits, complexes, membranes, or regulatory networks.
Study Non Model Plant Species
Support protein analysis using custom FASTA or transcriptome-derived sequence databases.
Integrate Proteomics and Metabolomics
Connect protein and metabolite changes for broader pathway and mechanism interpretation.
Choose the Right Plant Proteomics Workflow
Workflows can be combined or applied sequentially based on the study objective, enabling different proteomics strategies to complement one another within an integrated project design and support a more comprehensive analysis of the biological question.
Plant Quantitative Proteomics
Choose this workflow when You need DIA, TMT, or label-free proteomics to compare protein abundance across genotypes, treatments, tissues, or time points.
Click to preview →Plant Protein PTM Analysis
Choose this workflow when You need to characterize phosphorylation, acetylation, ubiquitination, glycosylation, or other supported plant protein modifications.
Click to preview →Plant Protein Interaction Analysis
Choose this workflow when You need IP-MS, Co-IP-MS, pull-down-MS, or proximity labeling to identify plant protein complexes and associated proteins.
Click to preview →Plant Metabolomics Analysis
Choose this workflow when You need untargeted metabolomics to broadly profile plant metabolites and compare metabolic responses across conditions.
Click to preview →Plant Proteomics and Metabolomics Analysis
Choose this workflow when You need to integrate protein and metabolite changes for pathway, phenotype, and mechanism interpretation.
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Workflow preview
Option One
Preview description for the selected option.
Service Workflow
Project Review
Confirm study design and samples.
Extraction
Extract proteins and remove contaminants.
Preparation
Digest proteins and prepare samples.
Acquisition
Acquire data by LC-MS/MS.
Data Processing
Identify, quantify, and analyze proteins.
Report
Deliver results, figures, and interpretation.
Project-specific extraction, database strategy, fractionation, and enrichment steps are selected according to tissue composition and study goals.
What to Send Us
| Sample Type | Recommended Input | Note |
|---|---|---|
| Soft plant tissue | 2 g | Soft tissues such as woody plant leaves or flowers, herbaceous plants, algae, ferns, and macrofungi. |
| Hard plant tissue | 5 g | Roots, bark, branches, fruits, seeds, and other tough or fibrous tissues. |
| Pollen | 100 mg | Submit clean pollen with minimal foreign material. |
Limited sample?
Send the amount you have. Final input is reviewed based on sample type, protein enrichment status, workflow, and required detection depth.
Results & Deliverables
Protein identification
Protein and peptide identification tables with database annotations, sequence evidence, and project-specific confidence metrics.
Quantitative matrix
Normalized protein or peptide abundance matrix for Label-Free, DIA, TMT, or quantitative PTM workflows as applicable.
QC & statistics
Identification and quantification QC, sample correlation, clustering or PCA, missing-value overview, and differential statistics.
Biological annotation
Gene Ontology, pathway, domain, subcellular localization, functional classification, and enrichment analysis based on available resources.
Visualization package
Publication-ready figures such as volcano plots, heatmaps, enrichment charts, clustering plots, and project-specific summaries.
PTM & interaction outputs
Site-level PTM tables, localization and motif information, or background-filtered interactor/proximity candidate tables when included in the project scope.
Platform & Capabilities
Project design & sample preparation
Start Project Review
Built for complex plant matrices
Preparation workflows are selected according to tissue composition, protein abundance, expected contaminants, and the downstream quantitative method.
Matrix-aware extraction
Tissue disruption and protein extraction strategies for leaves, roots, seeds, fruits, stems, woody tissues, callus, and cultured plant cells.
Contaminant control
Cleanup approaches for pigments, phenolics, polysaccharides, lipids, salts, detergents, and other LC-MS/MS-interfering components.
Database strategy
Species-specific, custom FASTA, transcriptome-derived, or homology-supported searching for model and non-model plants.
Design support
Guidance on groups, controls, replicates, batch balance, fractionation, PTM enrichment, bait selection, affinity capture, and interaction-background controls.
LC-MS/MS platform
High-resolution proteomics with integrated quality control
Orbitrap Exploris 480
High-resolution peptide identification and quantitative proteomics.
timsTOF Pro
Flexible acquisition for complex proteomes, PTM analysis, and interaction-proteomics characterization.
Orbitrap Astral
Robust high-resolution acquisition for comparative and DIA workflows.
Nano-LC Separation
Peptide separation optimized for sensitivity, reproducibility, and complex plant digests.
Extraction QCDigestion QCRetention-Time QCMS Performance QCReplicate CorrelationTransparent Data Tables
Applications of Plant Proteomics
Plant Stress and Environmental Response
Compare proteome changes under drought, heat, salinity, nutrient limitation, osmotic stress, or combined environmental stresses.
Plant Growth and Development
Study proteome and regulatory changes across tissues, developmental stages, and physiological transitions.
Genotype, Trait, and Comparative Proteomics
Compare cultivars, genotypes, phenotypes, mutants, or breeding materials with contrasting biological characteristics.
Integrated Proteomics and Multi-Omics Studies
Coordinate proteomics with metabolomics or other omics approaches when complementary molecular layers are needed to investigate complex plant phenotypes.
FAQs
Label-Free analysis supports flexible exploratory comparisons, DIA prioritizes consistent quantification across multiple samples, and TMT supports multiplexed group comparison. The final choice depends on sample number, group structure, input consistency, desired coverage, and the downstream analysis plan.
Yes. Projects may use a species-specific protein FASTA, transcriptome-derived database, custom sequence set, or a closely related reference when appropriate. Identification and functional annotation depth depend on the completeness and quality of the available sequence resources.
Collect samples consistently across groups, remove visible soil or medium when appropriate, snap-freeze as soon as practical, and store frozen to limit proteolysis and PTM loss. Avoid repeated freeze-thaw cycles and document collection time, treatment duration, and storage history.
Three or more biological replicates per group are commonly recommended for comparative studies, but the appropriate number depends on biological variability, experimental complexity, expected effect size, and the statistical questions being addressed.
Yes. Global proteome data can help distinguish changes in PTM abundance from changes in total protein abundance. Combined projects require sufficient sample input, coordinated group design, and a workflow matched to the PTM of interest.
Yes. LC-MS/MS-based proteomics can be used to characterize proteins in isolated plant extracellular vesicles or exosome-like nanovesicle preparations and, when the study design supports it, compare protein profiles across conditions. Because results are strongly influenced by vesicle isolation, sample purity, protein input, and background contamination, we recommend a feasibility review of the preparation method and available sample before analysis.
Proteomics can reveal protein-level changes, candidate regulators, PTM patterns, and interaction candidates that support a mechanistic hypothesis. Causal conclusions generally require orthogonal validation, genetic or biochemical experiments, and interpretation within the experimental model.
