Workflow

  1. Upload .RAW file(s); precursors are pooled across files.
  2. Pick a precursor; check the exhalation windows on the TIC and the isolation-window purity on the Precursor tab.
  3. Optional: lock-mass correction and the breath-phase filter (Fragments tab shows what it removes).
  4. Run SIRIUS; in Results click a formula, then a structure.

Terms

SIRIUS score Log-likelihood of the formula; compare candidates of one precursor, gaps < 1 are ties.
Explained Share of the MS/MS intensity the fragmentation tree explains.
Δ ppm Candidate mass vs the measured precursor (lock-mass corrected when the correction is applied).
P(iso) Fit of the candidate to the measured MS1 isotope envelope, normalised over the list. Shown only when the isotopes were measurable (status ok).
Purity Share of the MS1 ion current inside the isolation window carried by the selected precursor. Low purity = mixed (chimeric) MS/MS.
Co-isolated / above-precursor peaks Peaks inside the isolation window (except the precursor) and above the precursor m/z: co-isolated ions, not fragments of the precursor. Removed from the MS/MS only if the sidebar option is ticked.
Breath-phase class breath / background: fragment intensity higher / lower during exhalation (BH-adjusted Wilcoxon); flat: no difference; isolation window: unfragmented precursor ions.
CSI:FingerID / COSMIC Structure ranking within one formula / confidence that the top structure is correct.
CANOPUS Compound class predicted from the spectrum.
HMDB Number of HMDB structures with the formula (weak evidence either way).
Vol. Volatility class from the formula (Li et al.; VOC > 6.5 > IVOC > 2.5 > SVOC, log10 C*).
Excel export All candidates, details, settings and diagnostics of the run; bold = the app's recommendation. Do not re-save in Excel (checksum).
Extracted ion chromatogram
Isolation window (MS1)
MS2 scans
Precursor: measured − setpoint, by m/z
Precursor: measured − setpoint, over time
Mass error vs m/z, before / after correction
Instrument lock mass
Models (leave-one-out |p99|, ppm)
Anchors

            

            

              

                

                  
                

                

                  

                

              

              

                
Breath-phase ratio per fragment

                

              

              

                
Averaged MS/MS (what SIRIUS receives)

                

              

              

                
Fragments

                

              

              

            

            

              

                

                  

                    

                    

                      
Formula candidates

                      

                      

                    

                    

                      
HMDB structures with this formula

                      

                      

                    

                    

                      
Structures (CSI:FingerID)

                      

                      

                      

                    

                    

                      

                        
De novo structures (MsNovelist)

                        

                      

                    

                    

                      
Fragmentation tree

                      

                      

                      
                        
                        PNG
                      
                      

                    

                  

                  

                    

                      
Mirror plot

                      

                        
                        

                          
                          
                        

                      

                      

                    

                    

                      
Explained / unexplained peaks

                      

                    

                    

                      
Neutral losses

                      

                        
                        

                          
                          
                        

                      

                      

                    

                    

                      
CANOPUS classes

                      

                    

                    

                      
MS1 isotope pattern (P(iso))

                      

                    

                  

                

              

              

                
No results yet.

              

            

            

              

                
Workflow

                
    
                  
  1. Upload .RAW file(s); precursors are pooled across files.
    2. 
                  
  2. Pick a precursor; check the exhalation windows on the TIC and the isolation-window purity on the Precursor tab.
    3. 
                  
  3. Optional: lock-mass correction and the breath-phase filter (Fragments tab shows what it removes).
    4. 
                  
  4. Run SIRIUS; in Results click a formula, then a structure.
    5. 
                

                
Terms

                

                  
                    

                      SIRIUS score
                      Log-likelihood of the formula; compare candidates of one precursor, gaps < 1 are ties.
                    

                    

                      Explained
                      Share of the MS/MS intensity the fragmentation tree explains.
                    

                    

                      Δ ppm
                      Candidate mass vs the measured precursor (lock-mass corrected when the correction is applied).
                    

                    

                      P(iso)
                      Fit of the candidate to the measured MS1 isotope envelope, normalised over the list. Shown only when the isotopes were measurable (status ok).
                    

                    

                      Purity
                      Share of the MS1 ion current inside the isolation window carried by the selected precursor. Low purity = mixed (chimeric) MS/MS.
                    

                    

                      Co-isolated / above-precursor peaks
                      Peaks inside the isolation window (except the precursor) and above the precursor m/z: co-isolated ions, not fragments of the precursor. Removed from the MS/MS only if the sidebar option is ticked.
                    

                    

                      Breath-phase class
                      breath / background: fragment intensity higher / lower during exhalation (BH-adjusted Wilcoxon); flat: no difference; isolation window: unfragmented precursor ions.
                    

                    

                      CSI:FingerID / COSMIC
                      Structure ranking within one formula / confidence that the top structure is correct.
                    

                    

                      CANOPUS
                      Compound class predicted from the spectrum.
                    

                    

                      HMDB
                      Number of HMDB structures with the formula (weak evidence either way).
                    

                    

                      Vol.
                      Volatility class from the formula (Li et al.; VOC > 6.5 > IVOC > 2.5 > SVOC, log10 C*).
                    

                    

                      Excel export
                      All candidates, details, settings and diagnostics of the run; bold = the app's recommendation. Do not re-save in Excel (checksum).