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Qualitative Proteomics

1. Protein solution/gel: qualitative result table
2. Database Search Results
  2.1 List of peptide segments matched in the database search
  2.2 List of proteins matched in the database search
  2.3 List of modifications matched in the database search (phosphorylation, ubiquitination, etc.)
3. Raw data

Quantitative Proteomics (Label-Free/DIA/TMT)

1. Data Preprocessing
  1.1 Protein Database Search
2. Protein Expression Analysis
  2.1 Principal Component Analysis (PCA)
  2.2 Relative Standard Deviation (RSD)
  2.3 K-means Trend Distribution
  2.4 Reproducibility Evaluation
  2.5 Protein Expression Heatmap
3. Functional Annotation
  3.1 GO Functional Annotation
  3.2 KEGG Functional Annotation
  3.3 COG Functional Annotation
  3.4 GOslim Functional Annotation
  3.5 Pfam Protein Structure Domain Annotation
4. Protein Differential Analysis (biological replicates ≥ 3)
  4.1 Protein Differential Analysis Results
  4.2 Distribution of Differential Protein Fold Changes (FC)
  4.3 Statistical Analysis of Differential Protein Quantity
  4.4 Differential Protein Volcano Plot
  4.5 Differential Protein Clustering Heatmap
  4.6 Differential Protein GO Functional Annotation and Enrichment Analysis
  4.7 Differential Protein KEGG Functional Annotation and Enrichment Analysis
  4.8 Differential Protein COG Functional Annotation
  4.9 Differential Protein GOslim Annotation and Enrichment Analysis
  4.10 Differential Protein Structure Domain Annotation and Enrichment Analysis
5. Protein Network Interaction Analysis
6. Protein Reactome Pathway Annotation
7. Signal Peptide Prediction
8. Subcellular Localization of Proteins

Quantitative Proteomics (PRM)

1. PRM Protein Quantification Results
  1.1 Overview of Quantification Results
  1.2 Distribution of Fragment Ion Peak Areas for Peptide Segments

Quantitative Proteomics
* Protein Expression Analysis

↑Principal Component Analysis (PCA) 

 ↑Relative Standard Deviation (RSD)

  ↑K-means Trend Distribution

 
  ↑Correlation Analysis of Protein Expression Levels

  ↑ Protein Expression Heatmap

* Functional Annotation

  ↑GO Functional Annotation

  ↑ KEGG Functional Annotation 

↑ COG Functional Annotation

  ↑ GOslim Functional Annotation

  ↑ Pfam Protein Structure Domain Annotation
* Protein Network Interaction Analysis

↑ Protein Network Interaction Analysis

* Signal Peptide Prediction

↑ Signal Peptide Prediction

* Subcellular Localization of Proteins

↑Subcellular Localization of Proteins