setup, logs performance, and ensures timely maintenance.

QA: Ensures all records of system setup and configuration are reviewed for compliance.

4. Accountability

The Head of Bioanalytical Lab is accountable for ensuring mass spectrometers are properly set up, verified, and maintained in alignment with regulatory and quality standards.

5. Procedure

5.1 Pre-Setup Checklist

1. Ensure the instrument has completed its regular maintenance schedule (check maintenance log).
2. Confirm environmental controls (room temperature 20–25°C, humidity 40–60%) are within limits.
3. Check nitrogen gas supply, pump oil levels, and voltage supply (UPS backup status).

5.2 Power-Up Sequence

1. Turn on the roughing pump and allow stabilization (5–10 minutes).
2. Switch on the mass spectrometer’s main power and ion source heater.
3. Activate source gases (Nebulizer, Curtain, Ion Spray) per instrument specs.

5.3 LC Integration and System Connection

1. Connect LC flow path (from column outlet) to MS ionization source (e.g., ESI probe).
2. Check that there are no leaks or blockages in capillaries and ferrules.
3. Ensure the autosampler and pump are calibrated and set to desired flow rate (e.g., 0.5 mL/min).

5.4 Ion Source Configuration

1. Select appropriate ion source: Electrospray Ionization (ESI) or Atmospheric Pressure Chemical Ionization (APCI).
2. Adjust parameters:
   • Ion Spray Voltage: 4000–5500 V (ESI)
   • Source Temperature: 400–500°C
   • Curtain Gas: 25 psi
   • Nebulizer Gas: 50 psi
3. Load method file with predefined compound parameters (from validation protocol).

5.5 Calibration and Tuning

1. Infuse tuning solution (e.g., PPG, reserpine) using a syringe pump.
2. Perform mass calibration using standard ions:
   • Low Mass: 118.1 m/z
   • Mid Mass: 622.0 m/z
   • High Mass: 1222.0 m/z
3. Check peak intensity, resolution, and mass accuracy < ±0.1 Da.
4. Save calibration and tuning results in Annexure-1: MS Setup Log.

5.6 System Suitability Test (SST)

1. Inject system suitability standard (SSS) under validated LC-MS/MS conditions.
2. Verify:
   • Peak area RSD < 5%
   • Retention time within ±2%
   • S/N ratio meets minimum acceptance criteria
3. If SST fails, investigate and document in Annexure-2: SST Deviation Log.

5.7 Data File Management

1. Assign unique file path and batch name for each sequence.
2. Ensure raw data are automatically saved in designated secure directories.
3. Backup data on a daily basis to validated storage media/server.

5.8 Shutdown Procedure (if not in use)

1. Stop LC flow and flush system with water/acetonitrile mixture.
2. Switch off ion source gases and power down MS components in reverse sequence.
3. Log off software and note instrument status on Annexure-3: Instrument Status Record.

6. Abbreviations

• BA/BE: Bioavailability/Bioequivalence
• MS: Mass Spectrometry
• LC: Liquid Chromatography
• ESI: Electrospray Ionization
• SST: System Suitability Test

7. Documents

1. MS Setup Log – Annexure-1
2. SST Deviation Log – Annexure-2
3. Instrument Status Record – Annexure-3

8. References

• ICH M10: Bioanalytical Method Validation
• Instrument Operating Manual (e.g., SCIEX, Agilent, Thermo)
• FDA Guidance for Industry: Bioanalytical Method Validation

9. SOP Version

Version: 2.0

10. Approval Section

	Prepared By	Checked By	Approved By
Signature
Date
Name
Designation
Department

11. Annexures

Annexure-1: MS Setup Log

Date	Instrument ID	Ion Source	Tuning Compound	Setup By
17/04/2025	MS-003	ESI	PPG	Sunita Reddy

Annexure-2: SST Deviation Log

Date	Run ID	Issue Observed	Corrective Action	Reviewed By
17/04/2025	BE-MS-101	Low S/N ratio	Re-tuned ion source	Rajesh Kumar

Annexure-3: Instrument Status Record

Date	Status	Comment	Logged By
17/04/2025	Standby	Awaiting next batch	Vinay Pawar

Revision History:

Revision Date	Revision No.	Details	Reason	Approved By
01/01/2022	1.0	Initial release	New SOP	QA Head
17/04/2025	2.0	Expanded shutdown sequence and calibration standards	Audit Compliance	QA Head