LC-MS System — Standard Operating Procedure

1. Pre-Operation Checks

• [ ] Verify calibration status (mass accuracy check)
• [ ] Check N₂ gas supply (≥99.999%)
• [ ] Confirm source cleanliness
• [ ] Verify LC flow before connecting to MS
• [ ] Check waste line

2. System Calibration

1. Prepare calibration solution (NaI/CsI or commercial calibrant)
2. Infuse at 10 µL/min into source
3. Acquire calibration spectrum
4. Verify mass accuracy <5 ppm across range
5. Document calibration data

3. Sample Analysis

1. Dissolve peptide (1 – 10 µg/mL in 50% ACN/H₂O + 0.1% FA)
2. Infuse at 10 – 20 µL/min (direct infusion)
3. Acquire full scan spectrum (200 – 2000 m/z)
4. Deconvolute multiply charged envelope
5. Record observed monoisotopic mass

4. Data Interpretation

Parameter	Criteria
Mass Match	±0.5 Da of theoretical
Charge State Series	≥3 observed charge states
Signal Intensity	≥1×10⁵ counts
Adducts	Identify Na⁺, K⁺ adducts if present

5. Shutdown

1. Flush source with 50% ACN/H₂O (5 min)
2. Switch MS to standby
3. Turn off N₂ supply
4. Log instrument usage