HMS Analytical Chemistry Core

Located at 250 Longwood Ave; SGM Building Room 636

There is an Agilent 6530 QTOF LCMS and an Agilent 6130 Single Quad LCMS available for use by investigators who can operate them independently after a short training session. We expect users of the instruments to run their own samples and interpret the results. For access to the facility and to request training on either instrument, please submit an Application. If you require a higher level of service for small molecule analysis, please consider contacting the Small Molecule Mass Spectrometry Facility on the Harvard main campus. 

The instruments in the Analytical Chemistry Core are set up for small molecule analysis only at this time. If you are interested in pure protein mass spectrometry analysis, please visit the Thermo Fisher Center for Multiplexed Proteomics or the Taplin Biological Mass Spectrometry Facility both located in the HMS Cell Biology Department. 

LCMS & QTOF Training Application

Fee Summary

Fee Summary

A fee is charged for access to the Analytical Chemistry Core and the use of the instruments. These fees will help recover a portion of the costs associated with the operation and maintenance of the instruments. The Analytical Chemistry Core fees (and associated Facilities and Administration (F&A) fees) are revised annually based upon the Harvard Fiscal Year (July 1 - June 30). The fee structure is updated on the ACC website as soon as it is available. All charges are based on the fee at the time of service, not a previously provided estimate or price stucture from a previous fiscal year.

The HMS BCMP Department will invoice users on a regular (monthly) basis. 

Fees below are the anticipated rates for FY19 and apply to trainings and usage hours carried out in FY19 (July 1, 2018 - June 30, 2019); they are awaiting School approval to be finalized.

A per user fee of $125 will be charged for a one hour training session per instrument. If additional training is necessary, it will be billed at the hourly rate for the appropriate instrument.

  HMS Internal Quad Investigators HMS-Affiliated and Non-Harvard Academic Investigators (Includes F&A)
QTOF Fee per Hour
LCMS Fee per Hour



Agilent 6530 QTOF Mass Spectrometer with 1290 Infinity Binary LC (Mass accuracy 1 ppm with internal calibrant).

See the 'Fees Summary' drop down list for the fees associated with training and usage on the QTOF. 


Agilent 6130 Single Quadrupole Mass Spectrometer with 1260 LCMS

See the 'Fees Summary' drop down list for the fees associated with training and usage on the LCMS


Facility Rules

  1. These instruments are intended only for analysis of small molecules derived from synthetic reactions or natural product extracts.
  2. New users must complete the online Application form. All users of the facility must be trained by the facility manager or an Agilent application specialist. Your ID will not be activated to the facility until your training has been completed.
  3. All users must go through the Lab Specific Safety Checklist with the facility manager and sign the form before their ID can be activated for the room. ID access is NOT transferrable to others. 
  4. Users must provide their own column, which is dedicated to LCMS use.
  5. LCMS solvents are supplied and located in the flammable cabinet. Please return solvent bottles to the flammable cabinet after use.
  6. Use only LCMS grade solvents on both instruments.
  7. Do not inject samples containing high salt or high detergent, or samples dissolved in DMSO.
  8. Do not modify the parameters for the mass spectrometer without consulting the facility manager.
  9. Check the liquid nitrogen tanks, if you replace a tank with a backup, please notify the operations coordinator or facility manager to ensure a replacement is ordered.


Once you have been trained on an instrument and completed the lab safety checklist, an account for scheduling time on the instrument will be created for you in PPMS. Sign up for time using PPMS online scheduling system.

Monday-Friday: 8 AM – 5 PM:  Maximum 3 hours
Overnight 5 PM – 8 AM: No limit

Saturday-Sunday: 8 AM-5 PM: Maximum 5 hours
Overnight 5 PM – 8 AM: No limit

Please be considerate of your fellow users. Only sign up for as much time as you need, be punctual, and clean up when you are done.

Contact Information

For instrument access and approval requests: (Operations Coordinator)

For instrument training and specific usage questions: (Facility Manager and Instrument Specialist)