LCMS Analysis at Bakar Labs

Bakar Bio Labs has two LCMS instruments (liquid chromatograph mass spectrometers) in our Specialized Equipment Rooms. Access to these rooms can be requested via Freshdesk ticket.

• Room 128: Single-quadrupole with diode array detector (Agilent 1200-series InfinityLab Pro iQ)

• Room 505: Quadrupole Time-of-Flight (Agilent 6545XT AdvanceBio LC/Q-TOF)

  • Note: There is a monthly access fee per company of $500 to use the LC/Q-TOF instrument. This is in addition to the per person fees to access the Specialized Equipment Rooms.

Generally, the single-quadrupole instrument is appropriate for routine LCMS analysis where your analyte has a strong UV absorbance or unique mass-to-charge ratio (m/z) that a good signal-to-noise ratio compared to baseline.

The QTOF is appropriate for discovery work, proteomics workflows, or where you have multiple co-eluting analytes with similar (though not identical) m/z ratios. After your discovery work on the QTOF, you may want to consider shifting your routine sample runs to the single-quadrupole instrument downstairs.

Note: QB3 Berkeley has two mass spectrometry cores on campus. More information can be found HERE.

To gain access to either instrument, follow these steps:

1. Submit a Freshdesk ticket to to discuss your proposed usage of either instrument. Make sure to include your past experience with the LCMS analysis and the following details of your method:
   

   • Analyte and sample matrix

   • Column type

   • Mobile phases

   • Sample volume and run frequency

   • Approximate method runtime 

   • Detection method: Diode Array Detector (DAD for UV detection) and/or Single-Quad MS or QTOF MS

2. LabOps staff will evaluate your responses and determine if your plan is compatible with the current users of the instruments and the instrument configuration. We may consult with Agilent technical support if needed.

3. Read, understand, and sign the SOP (link will be included in the emailed response from Lab Ops).

4. If you are new to Agilent LCMS instruments, the LabOps team can provide log-in information to Agilent University. We recommend starting with these two on-demand courses:

   1. LCMS-6100-1102e - Tuning Agilent Single Quadrupole LC/MSD iQ System in OpenLab CDS

   2. LCMS-6100-2120s - Agilent LC/MSD iQ: How to Build Acquisition Methods Using Auto Acquire and Advanced Acquire in OpenLab CDS

5. If you have additional training needs, please reach out to Nicole Catly (nicole.catly@agilent.com) and mention you are with a company at Bakar Labs.