Post-translational modifications (PTMs) are the protein chemical modifications that extend the function and diversity of the protein, thus increasing the complexity of the proteome. These processes occur on almost all proteins that are simultaneously modified by different PTMs at multiple sites. Functional analysis aims to bring the quantitative PTM analysis into the biological context and interpret data at the biological level based on annotations, protein subcellular localization, protein structural properties, protein interactions, or metabolic fluxes. Creative Proteomics specializes in protein PTM bioinformatics analysis services and offers a wide range of services including PTM functional analysis. Our service is based on a variety of popular functional analysis tools, enabling fast and targeted research while still providing an in-depth overview of the potential role of PTMs in cellular processes.
Overview of the PTM functional analysis
PTMs play a key role in many cellular processes, and there is a growing number of studies suggesting that dysregulation of PTMs is associated with the development and progression of various diseases. After identifying and quantifying protein PTMs, we need to understand the complex circuitry of cell signaling affected by PTMs. Over the past few decades, a number of methods have been developed for PTM functional analysis, and we provide an overview of them.
| Methods currently available for PTM functional analysis |
|---|
| Terms | Applications | Representative tools |
|---|
| PTM annotation | Classify the identified PTMs from the functional levels and understand the up/down regulated process. | PANTHER Pathway
Uniprot
KEGG |
| Protein 3D structure | Help understand the spatial layout and function. | Protein Data Bank(PDB)
PTM-SD
DisoPred software |
| Protein interaction | Reveal the relationship between groups of modified proteins. | STRING
NetworkKIN
PTMOracle
Cytoscape |
| Motif analysis | Identify and discover the significant or new motifs, suggesting the types of enzymes involved. | Motif-x
PhosphoMotif
iceLogo
PTMphinder |
| Signaling network analysis | Insight into PTM functions and discover novel pathways or networks, exploring the regulatory modification pattern of proteins. | STRING
SIGNOR
KEGG
PhosphoSitePlus
Reactome |
PTM functional analysis service
Based on years of experience in protein PTM bioinformatics analysis and advanced platforms, we are able to perform PTM functional analysis for our clients worldwide. We have established an integrated database to examine the function and co-occurrence of protein PTMs in both animals and plants. Our powerful services support the sharing and visualization of PTM data (including phosphorylation, ubiquitinylation, acetylation, etc.) from mass spectrometry (MS) experiments, the development of hypotheses related to target proteins, or the identification of patterns of signaling and metabolic pathways in PTM data. The resulting network visualizations and all underlying PTM data are easily accessible for further analysis or distribution. More importantly, our services are driven by customer demand, a solid scientific foundation, and popular bioinformatics tools that advance PTM functional analysis.
- Functionally analyze PTMs in individual proteins.
- Functionally analyze PTMs in protein complexes.
- Functionally analyze PTMs in groups of proteins that are co-modified by multiple user-defined PTMs.
Our service support
- PTM functional annotation.
- PTM functional enrichment analysis.
- PTM functional clustering analysis.
- PTM functional classification.
Our service allows researchers and professionals to quickly evaluate basic information about PTMs related to their proteins of interest, dig deeper into the capabilities of PTMs, and quickly submit results data. For more information on our PTM functional analysis service, please use our contact form. Our professional staff looks forward to working with you on your next project.
Related services
References
- Chen, Chen, et al. "Bioinformatics methods for mass spectrometry-based proteomics data analysis." International Journal of Molecular Sciences 21.8 (2020): 2873.
- Pascovici, Dana, et al. "Clinically relevant post-translational modification analyses—maturing workflows and bioinformatics tools." International journal of molecular sciences 20.1 (2018): 16.
Our products and services are for research use only.
