Plant Proteome Bioinformatics Analysis Platform

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Plant Proteome Bioinformatics Analysis Platform

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CD BioSciences provides plant proteome bioinformatics analysis platforms. We can screen and search for critical proteins and signaling pathways, and perform validation of related functions. Our platform can help clients deeply analyze proteomics data, essential for guiding subsequent functional research.

What is Proteomics Bioinformatics Analysis?

Proteomics data analysis usually involves finding differentially expressed proteins by comparing the expression of proteins in samples; finding biological functions and signaling pathways that are significantly enriched by differentially expressed proteins through functional annotation and enrichment analyses; and performing protein interaction network analyses of differentially expressed proteins to demonstrate the interconnections between differentially expressed proteins, thereby finding critical nodes in the network.

Integrated proteomic workflows. Figure 1. Integrated proteomic workflows. (Schmidt, A.,et al., 2014)

Platform Content

Proteomics or modifiers analysis

Platforms Details
Differential analysis platform We use statistical analysis to accurately identify proteins or modification sites that undergo significant changes, thereby researching biological regulatory mechanisms and laying the foundation for subsequent analysis.
Protein function enrichment analysis platform Our enrichment analysis platform uses Fisher's test to detect whether the function set is enriched in differential proteins, including protein structural domains, gene ontology functions, KEGG pathways, complexes, etc.
MS data quality control platform We perform quality control on MS data to ensure compliance with standards. Including the distribution of peptide length and number, parent ion mass tolerance, protein coverage, and protein molecular weight.
Protein function clustering analysis platform We further clustered the results based on the enrichment analysis, clustered the relevant functions of different comparison groups together, and plotted heat maps.
Motif analysis platforms for modification sites We use Motif-x or iceLogo analysis to predict potential motif signatures of modification sites and extract statistically significant biological motifs from around post-translational modification sites.
Protein functional classification platform Our protein function annotation based on the COG/KOG database can accurately identify orthologs and paralogs, which is a clear advantage for functional annotation of newly sequenced species.
Repeatability analysis platform Our platform evaluates the consistency of results from multiple replicates, including Principal Component Analysis (PCA), Relative Standard Deviation (RSD), and Pearson correlation.
Protein functional annotation platform We functionally annotate proteins of interest to facilitate clients' understanding of the various biological significance of plant proteins. Including gene ontology functions, KEGG pathways, protein structural domains, subcellular localization, complexes, and COG/KOG annotations.

Proteome and metabolome association analysis

We performed Spearman correlation analysis on differential proteins and metabolic molecules and further constructed correlation networks. After KEGG enrichment analysis, proteomic and metabolomic interaction network analysis is performed using Cytoscape.

Macroproteome analysis

We combine cutting-edge technologies such as off-specification quantification, HPLC classification, and MS-based quantitative proteomics to perform quantitative macro-proteomics research.

Personalized biosignature analysis

  • Protein interaction network function module analysis
  • WGCNA analysis
  • Modification site conservation analysis
  • Survival analysis
  • Modification site homology analysis
  • Phosphokinase analysis
  • PSEA analysis
  • Molecular typing
  • PTM-SEA analysis
  • Biomarker prediction analysis

CD BioSciences is dedicated to providing a comprehensive platform for plant proteome bioinformatics analysis. We utilize cutting-edge computational tools and algorithms to help researchers explore the vast promise of plant proteomics. If you are interested in our platform, please feel free to contact us. Our advanced technology allows you to effectively analyze and interpret complex plant proteomic data to reveal complex molecular mechanisms and functions.

Reference

  1. Schmidt, A., et al. (2014). Bioinformatic analysis of proteomics data.BMC Systems Biology. 8 Suppl 2(Suppl 2), S3.

For research use only, not for clinical use.