PTM Proteomics

PTM proteomics systematically characterizes the types, sites, and dynamics of protein post-translational modifications across the proteome. Deep phosphoproteomics provides large-scale quantiatitative analysis of protein phosphorylation sites and is a useful tool to define signaling network regulation and dysregulation.

Protein phosphorylation is one of the most common and important PTMs. This reversible mechanism occurs through protein kinases and consists of the addition of a phosphate group (PO4) to the polar group R of various amino acids (eg. serine/S, threonine/T, or tyrosine/Y). Phosphorylation is the primary mechanism driving cellular signal transduction. It governs everything from cell cycle progression, apoptosis, and growth to complex metabolic regulation and immune responses. Mapping these systems is a cornerstone of biomedical research.

Novogene provides deep phosphoproteomics services with the Obitrap Astral platform with a throughput of 60 samples per day (60 SPD).The workflow encompasses protein extraction, digestion, enrichment, desalting, instrumental analysis, and data processing with a turnaround time of 4 weeks.

Why Choose Novogene for Your PTM Proteomics Needs?

Deep & High-Accuracy PTM Site Identification

In-depth analysis of PTMs that decodes "dark matter" of life regulation with increased depth of site identification and Improved accuracy of site identification (Class I sites ≥ 90%).

Precise Modification Localization & Dynamic Quantification

Multi-dimensional analysis and annotation that precisely localizes modification sites and quantifies dynamic fluctuations.

Multi-Dimensional Functional Decoding of PTMs

Multi-dimensional functional decoding through the analysis of domains, kinase prediction, interaction networks, disease associations, etc. to transform high-dimensional data into functional catalogues.

Applications

Novogene delivers high-quality data and publication-ready analysis results of deep phosphoproteomics to faciliate research including:

Regulation of protein function

PTMs precisely control protein activity, stability, localization, and interactions. This allows cells to dynamically fine-tune protein behavior in response to stimuli, regulating essential processes from signal transduction and metabolism to gene expression.

Enzyme regulation

PTMs directly regulate enzyme activity. For instance, phosphorylation can activate or inhibit catalytic function, thereby controlling key cellular signaling and metabolic pathways.

Cell signaling

PTMs are central to cellular communication. Modifications (like phosphorylation) act as molecular switches that turn proteins "on" or "off," enabling cells to relay and respond to signals effectively.

Disease biomarkers

Aberrant PTM patterns are directly linked to diseases such as cancer and neurodegenerative disorders. Detecting these altered PTMs provides valuable biomarkers for improved diagnosis, prognosis, and drug target identification.

Drug development

Understanding PTMs enables the design of targeted therapies. Modifying specific PTMs can restore normal protein function and cellular processes, presenting promising new therapeutic strategies.

Applications

Novogene delivers high-quality data and publication-ready analysis results of deep phosphoproteomics to faciliate research including:

Regulation of protein function

Enzyme regulation

PTMs directly regulate enzyme activity. For instance, phosphorylation can activate or inhibit catalytic function, thereby controlling key cellular signaling and metabolic pathways.

Cell signaling

Disease biomarkers

Drug development

Understanding PTMs enables the design of targeted therapies. Modifying specific PTMs can restore normal protein function and cellular processes, presenting promising new therapeutic strategies.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Overview of Data Processing and Bioinformatic Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Project Workflow

Novogene provides high-quality products and expert services throughout the entire project workflow. From sample preparation to data acquisition, every step in the process-including protein extraction, quantification, detection, enzymatic digestion, modified peptide enrichment and desalting, and mass spectrometry analysis can influence the quality of the data. To ensure accurate and reliable results, Novogene maintains tight control over each step, fundamentally safeguarding data quality. The experimental workflow is provided below.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Sample Type		Amount
Animal tissues	General tissue (brain, heart, liver, spleen, lung, kidney, muscle, etc.)	100 mg
Plant tissues	Soft tissues (leaves, flowers, algae, ferns, etc.)	500 mg
	Fruit pulp	1 g
	Seeds	5 g
	Pollen	4 g
Cells	Suspension/Adherent cultured cells	400 μL
Microorganisms	Common bacteria	2×107 (50 μL cell pellet)
Microorganisms	Fungal mycelium	200 mg or 200 μL pellet

Overview of Data Processing and Bioinformatic Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Project Workflow

Resources

1/1

Phosphorylated kinase site expression level chart

For the identified phosphosites, the kinases involved in phosphorylation process were predicted. Top 100 kinases with the highest prediction scores were selected for quantitative analysis.

1/1

The volcano plot of the differential phosphosites

For each differential phosphosite, the fold change is taken as the log2 value, and the P-value is taken as the absolute value of the log10 value to create a volcano plot.

1/1

The HCA heatmap of the differential phosphosites

The HCA heatmap of the differential phosphosites. A Hierarchical Cluster Analysis (HCA) heatmap is used to illustrate the up-regulation and down-regulation of different phosphosites when comparing different samples.

1/1

The bar chart of the number of upregulated and downregulated modification site-corresponding proteins

Based on the GO enrichment results in this project, the bar charts were plotted to compare the numbers of upregulated and downregulated proteins corresponding to the differential modification sites enriched in GO.

1/1

The annotation of differential phosphosite-associated proteins in enriched KEGG pathway

In the map, the differential phosphosite-associated proteins are highlighted.

1/1

The bubble plot of domain enrichment

Protein domain enrichment analysis can identify statistically significantly enriched domain entries. These functions or locations may be the reasons for the differences.

Resources

1/1

Phosphorylated kinase site expression level chart

For the identified phosphosites, the kinases involved in phosphorylation process were predicted. Top 100 kinases with the highest prediction scores were selected for quantitative analysis.

1/1

The volcano plot of the differential phosphosites

For each differential phosphosite, the fold change is taken as the log2 value, and the P-value is taken as the absolute value of the log10 value to create a volcano plot.

1/1

The HCA heatmap of the differential phosphosites

1/1

The bar chart of the number of upregulated and downregulated modification site-corresponding proteins

1/1

The annotation of differential phosphosite-associated proteins in enriched KEGG pathway

In the map, the differential phosphosite-associated proteins are highlighted.

1/1

The bubble plot of domain enrichment

Protein domain enrichment analysis can identify statistically significantly enriched domain entries. These functions or locations may be the reasons for the differences.