Proteomics Data Analysis in R/Bioconductor
Welcome!
1
Isobaric Quantification Pipelines
1.1
Global Proteomics Data
1.1.1
Read MS-GF+ Data
1.1.2
Correct Isotope Selection Error
1.1.3
Remove Contaminants
1.1.4
MS/MS ID Filter: Peptide Level
1.1.5
MS/MS ID Filter: Protein Level
1.1.6
Inference of Parsimonious Protein Set
1.1.7
Remove Decoy PSMs
1.1.8
Read MASIC Output
1.1.9
Filter MASIC Data
1.1.10
Create Study Design Tables
1.1.11
Fractions
1.1.12
Samples
1.1.13
References
1.1.14
Create Quantitative Cross-tab
1.1.15
Create MSnSet Object
1.2
Phosphoproteomics Data
1.2.1
Read MS-GF+ Output
1.2.2
Correct Isotope Selection Error
1.2.3
Remove Non-Phosphorylated Peptides
1.2.4
Remove Contaminants
1.2.5
Improve Phosphosite Localization
1.2.6
MS/MS ID Filter: Peptide Level
1.2.7
MS/MS ID Filter: Protein Level
1.2.8
Inference of Parsimonious Protein Set
1.2.9
Remove Decoy PSMs
1.2.10
Map Sites to Protein Sequences
1.2.11
Read MASIC Output
1.2.12
Filter MASIC Data
1.2.13
Create Study Design Tables
1.2.14
Create Quantitative Cross-tab
2
Label-Free Quantification
3
Exploratory Data Analysis
3.1
Count Features in Samples
3.2
Estimate Blood Contamination
3.3
PCA
4
Heatmaps
4.1
Expression Heatmaps
4.2
Correlation Heatmaps
4.2.1
Sample Correlation
4.2.2
Feature Correlation
4.3
Heatmap Annotation
4.3.1
Modifying Default Colors
4.4
Modifications
4.4.1
Row and column labels
4.4.2
Label colors
4.4.3
Label specific features
4.4.4
Heatmap body color
4.4.5
Horizontal heatmaps
4.4.6
Legends
5
Linear Modeling
5.1
Multiple Comparisons
5.2
Linear Regression
5.3
Two-Sample t-tests
5.3.1
One comparison
5.3.2
Multiple comparisons
5.4
One-Way ANOVA
5.5
p-value Histograms
5.6
Volcano Plots
6
Pathway Analysis
6.1
Annotation Databases
6.1.1
Gene Ontology
6.1.1.1
Semantic Similarity
6.1.1.2
GO Subsets/Slims
6.1.2
Reactome
6.1.3
KEGG
6.1.4
Pfam
6.2
Over-Representation Analysis
6.2.1
Overview
Important Considerations
6.2.2
Examples
6.2.2.1
Gene Ontology
6.2.2.2
Reactome
6.2.2.3
Pfam
6.2.2.4
Other Databases
6.3
Gene Set Enrichment Analysis
6.3.1
Overview
Important Considerations
6.3.2
Examples
6.3.2.1
Gene Ontology
6.3.2.2
Reactome
6.3.2.3
Pfam
6.3.2.4
Other Databases
References
Proteomics Data Analysis in R/Bioconductor
Section 1
Isobaric Quantification Pipelines