1. Full Scan MS

1.1 Principle

• Q1 (quadrupole) remains in wide-pass mode.

• All ions enter the TOF analyzer without precursor selection.

• Provides high-resolution, accurate-mass MS1 spectra.

1.2 Typical Applications

• Unknown compound discovery

• Accurate mass measurement / formula prediction

• PFAS initial screening

• Chemical profiling of environmental samples

1.3 Advantages & Limitations

✔ Comprehensive, unbiased data
✔ Excellent mass accuracy
✘ No MS/MS → limited structural information

2. Targeted MS/MS

2.1 Principle

• Q1 isolates a specific precursor ion (e.g., m/z 413 for PFOA).

• Collision cell fragments the precursor at selected CE.

• TOF records high-resolution product-ion spectra.

2.2 Applications

• Confirming identity of known analytes

• Targeted PFAS analysis

• Drug/metabolite verification

• Quantitative confirmation workflows

2.3 Characteristics

✔ Strong diagnostic fragments for confirmation
✔ Highest selectivity for known targets
✘ Not suitable for unknown compounds

3. Auto MS/MS (DDA: Data-Dependent Acquisition)

3.1 Workflow

• Perform a full MS scan.

• Software automatically selects “Top N” most intense ions.

• Trigger MS/MS on each selected precursor.

• Apply dynamic exclusion to avoid repeated fragmentation of the same ion.
  
  

3.3 Best-Fit Applications

• Structural elucidation of unknown PFAS

• Metabolite discovery

• Environmental unknown screening

• Complex mixture analysis
  
  

3.4 Pros & Cons

✔ Automated, discovery-oriented
✔ Provides MS/MS for many compounds
✘ High-flow separations may miss fast eluting peaks
✘ Can generate redundant or biased fragmentation