Sort Order:
(Applies to Sample Metrics)
Detected vs Inferred Proteins per Sample
Precursor Evidence Heatmap (Top 50 Most Variable)
Cumulative Detection Curve
Sample Clustering by Detection Pattern (Jaccard Distance)
Precursor Count per Protein (per Sample)
No TIC data available. Extract from the Search tab before searching, or use the button below to extract from an existing output directory.
Color by:
Viewing Comparison:
Tip: Assign experimental groups (required). Covariate columns are optional - customize names and include in model as needed.
Export
Covariates:
Viewing Comparison:
CSV
Per-Group Replicate Statistics
Contaminant Protein Analysis
Per-Sample Contaminant Intensity
Top Contaminant Proteins
Contaminant Expression Heatmap (Top 20)
Viewing Comparison:
💾 Export Full Table

Data Explorer

Export for Claude
Abundance Profiles (Quartile Analysis)
Proteins split into quartiles by average intensity. Colors show per-sample quartile assignment. Proteins that change quartile across samples may be biologically interesting.
Variable Proteins (Quartile Range >= 2)
Sample-Sample Scatter

AI-Powered Analysis Summary

How it works: Click the button below to generate a comprehensive AI-powered analysis across all comparisons in your experiment.

The AI will identify key DE proteins per comparison, cross-comparison biomarkers, and provide biological insights on high-confidence candidates.

Viewing Comparison:
Heatmap of Selected/Top Proteins
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💾 Export
Color by:
Axes:
PNG
CSV

Distribution of Coefficient of Variation (CV) for significant proteins, broken down by experimental group.

PNG 

                      

                      
                    

                    
Enrichment analysis on DE results. Auto-detects organism. Results cached per ontology.

                  

                  
                

                

                  

                    
                  

                  

                    

                      

                        

                          
                            
                            
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Configure Comparison

                      
                    

                    

                      

                        

                          
                          

                            

                              
                            

                            

                              
                            

                            

                              
                            

                          

                        

                      

                      

                        

                          
                          

                            

                              
                            

                            

                              
                            

                          

                        

                        

                          

                            
                            

                              
                              
                            

                            

                              

                            

                          

                        

                      

                      

                        

                          

                            
                            

                              
                              
                            

                            

                              

                            

                          

                        

                        

                          

                            
                            

                              
                              
                            

                            

                              

                            

                          

                          

                          

                            
                              Or upload individual files...
                            
                            

                              

                                
                                

                                  
                                  
                                

                                

                                  

                                

                              

                              

                                
                                

                                  
                                  
                                

                                

                                  

                                

                              

                            

                          

                          

                            
                              
                              Spectronaut Setup Guide
                            
                            How to export from Spectronaut
                          

                        

                        

                          

                            
                            

                              

                                
                              

                              

                                
                              

                            

                          

                          

                            

                              
                              

                                
                                
                              

                              

                                

                              

                            

                          

                          

                            

                              
                              

                                
                                
                              

                              

                                

                              

                            

                            

                              
                               Layers 1-3 only. 
                              Run FragPipe-Analyst for full DE comparison.
                            

                          

                        

                      

                    

                    

                      

                        
                          
                           Attach DIA-NN log files (optional — fills in search parameters)
                        
                        

                          

                            

                              
                               Upload 
                              report_log.txt
                               or the SLURM 
                              .out
                               file from each DIA-NN search. 
                              Only the command line and summary stats are read.
                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                  

                                    

                                  

                                

                              

                              

                                

                                  
                                  

                                    
                                    
                                  

                                  

                                    

                                  

                                

                              

                            

                            

                          

                        

                      

                    

                    

                    

                    

                      
                    

                  

                  

                    

                    

                      

                        
                      

                      

                        

                          

                            

                              

                                
                              

                              

                              

                              

                            

                          

                        

                        

                          

                            

                              

                                
                              

                              

                                

                                  

                                

                                

                                  

                                

                              

                              

                                
Protein Details

                                

                                  
                                  
                                  
                                  
                                

                                
                              

                              

                            

                          

                        

                        

                          

                            

                              

                                
                              

                              

                                

                                  

                                

                                

                                  

                                

                              

                              

                              

                            

                          

                        

                        

                          

                            

                              

                                
                              

                              

                            

                          

                        

                        

                          

                            

                              

                                
AI-Powered Comparison Analysis

                                
                              

                              
Generate an AI narrative summary or export data for external analysis.

                              

                                
                                
                                
                                  
                                  Export ZIP for Claude Analysis
                                
                              

                              

                              

                              
MOFA2 Factor Decomposition

                              

                                Treats Run A and Run B as two views of the same samples and decomposes 
                                joint variance into shared and run-specific factors.
                              

                              
                              

                                

                                

                                

                              

                            

                          

                        

                      

                      
                    

                  

                

              

              

                

                  

                    

                      Chat with Full Data (QC + Expression)
                      
                    

                  

                  

                    

                    

                    

                      

                        
                        
                      

                      
                      
                    

                    
Note: QC Stats (with Groups) + Top 800 Expression Data are sent to AI.

                  

                  
                

              

              

                

                  

                    

                      
                       Export Complete Analysis
                    

                    

                      Download everything needed to reproduce and share this analysis. 
                      Includes all data files, DIA-NN search parameters, and session state.
                    

                    

                      What's included (click to expand)
                      
    
                        
  • 
                          expression_matrix.csv
                           -- Normalized protein intensities (DPC-Quant, complete, no missing values)
                        
    • 
                        
  • 
                          diann_pg_matrix.tsv
                           -- DIA-NN protein-level matrix with real missing values (0 = not detected, ~200 KB)
                        
    • 
                        
  • 
                          data_quality_summary.csv
                           -- Per-sample protein counts, % detected, contaminant counts
                        
    • 
                        
  • 
                          detection_matrix.csv
                           -- Per-protein precursor detection counts per sample
                        
    • 
                        
  • 
                          quartile_profiles.csv
                           -- Intensity quartile assignments per sample
                        
    • 
                        
  • 
                          variable_proteins.csv
                           -- Proteins with inconsistent abundance across samples
                        
    • 
                        
  • 
                          sample_metadata.csv
                           -- Sample groups and identifiers
                        
    • 
                        
  • 
                          contaminant_summary.csv
                           -- Contaminant protein statistics
                        
    • 
                        
  • 
                          search_info.md
                           -- Full DIA-NN search parameters and job metadata
                        
    • 
                        
  • 
                          session.rds
                           -- Complete session state (reload in DE-LIMP)
                        
    • 
                        
  • 
                          methods.txt
                           -- Pipeline parameters, normalization, app version
                        
    • 
                        
  • 
                          reproducibility_log.R
                           -- R code log to reproduce every step
                        
    • 
                        
  • 
                          PROMPT.md
                           -- AI analysis prompt with biological questions
                        
    • 
                      

                    

                    
                      
                      
                       Export Complete Analysis ZIP
                    
                  

                  

                    

                      
                       DE Results Table
                    

                    

                      Quick export of the DE results for the selected comparison. 
                      Includes gene symbols, logFC, P.Value, adj.P.Val, and per-sample expression values. 
                      One CSV file — no search parameters or session data.
                    

                    
                      
                      
                       Export Results CSV
                    
                  

                  

                    

                      
                       CV Analysis
                    

                    

                      Coefficient of variation for significant proteins. 
                      Includes per-group CV and average CV values. One CSV file.
                    

                    
                      
                      
                       Export CV Analysis CSV
                    
                  

                  

                    

                      
                       Full DIA-NN Output
                    

                    

                      The complete DIA-NN search output (report.parquet, precursor matrices, spectral libraries, logs) 
                      is stored on the HPC cluster. These files can be large (100 MB+) and are not included in the analysis export.
                    

                    

                  

                

              

              

                

                  

                    
                  

                  

                    

                      

                        

                          
                           Action Log:
                          This code recreates your analysis step-by-step. Each section shows:
                          
    
                            
  • 
                              Action name
                               - what you did (e.g., 'Run Pipeline')
                            
    • 
                            
  • 
                              Timestamp
                               - when you did it
                            
    • 
                            
  • 
                              R code
                               - how to reproduce it
                            
    • 
                          

                          
Copy this entire code block to reproduce your analysis in a fresh R session.

                        

                        
                          
                          💾 Download Reproducibility Log
                        
                        

                      

                    

                    

                      

                        

                          
                        

                        

                          

                        

                      

                    

                  

                  
                

              

              

                

                  

                    
DE-LIMP

                    

                      
                    

                    
Differential Expression — LIMPA Pipeline

                  

                  

                  

                  

                  
                  

                

              

              

                

                  
Proteomics Resources & Training

                  

                    
                    
Explore video tutorials, training courses, and methodology citations.