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Mass Spectrometry Service


The facility offers mass spectrometry service with the following equipment, on a first-come-first-served basis:

Orbitrap Eclipse 1.png

Services Provided:

1. Shotgun Protein Identification

  • In-solution tryptic digestion and desalting service available

  • Database search using Proteome Discoverer software

2. Protein Quantification

  • Label-free Quantification

  • Parallel Reaction Monitoring (PRM)

  • Labeling Quantification by MS2 (up to 18-plex for TMT labels)

  • Labeling Quantification by RTS-SPS-MS3 (up to 18-plex for TMT labels)

3. Intact Protein Accurate Mass Measurement (<50kDa)

  • LC separation of proteins followed by accurate mass measurement

  • Mass deconvolution available

4. Direct infusion MS analysis for high purity samples

  • HCD, CID, ETD fragmentation modes

  • Multi-stage MS (MSn) analysis available


Services Provided:

1. Shotgun Protein Identification

  • In-solution tryptic digestion and desalting service is available

  • Database search using PEAKS Studio software

2. Protein Quantification

  • Label-free Quantification


3. Lipidomics

  • Database search using Bruker MetabScape software

How to apply for the service?

Please fill in the corresponding form in FULL and submit sample(s) during office hours.

Please refer to the form-filling guidelines for all three instruments here.

Details regarding sample submission can be found here.

For inquiries, please contact Ms. Joyce Wong at or Ms. Haity Ngan at


  • How do I get equipment access and/or apply for specialized services (mass spectrometry, sequencing & tissue processing)?"
    First, you have to register for an account on our online booking system to become an authorized user. To get access to self-service equipment, all users have to be trained (and in some cases, assessed) so that they can follow standard operation procedures and be aware of necessary safety precautions. They can register for training sessions on our booking system. For equipment that requires operation assessment, instructors will inform users of the assessment criteria during the training. After gaining access, users can enter the corresponding rooms where the equipment is located in and the main office of BioCRF (Room 6127) 24/7, unless emergencies arise. As for applying for specialized services, please read the guidelines on the following pages: 1. Sequencing 2. Mass Spectrometry 3. Tissue Processing
  • What rules must I be aware of as a BioCRF user?
    Only the specific authorized user (but not other untrained users from the same group or department) is allowed to use the facilities in BioCRF. When making equipment reservations, authorized users should abide by the booking restrictions and rules of the equipment. Authorized users should sign the log books as appropriate and report any issues to BioCRF staff. Authorized users should ensure that the equipment is clean and in good working order after use. Authorized users should download their experimental data from the server of BioCRF. USB sticks and hard disks on BioCRF computers (except computers designated for data analysis) are strictly prohibited. If users do not show up for their reservations, or if they arrive 15 minutes later than their reservation start time, they will receive a no-show warning. Users also receive a warning from misusing or damaging any equipment. Upon receiving two, their access to the equipment will be suspended for at least a month. Any cost of repair due to the misuse of equipment will be charged to the account of the user's supervisor. The supervisor should inform users about the University's safety and environmental policies, as well as safety statements, standards and procedures related to the user's experiment. The supervisor should also inform the user of any potential hazard and safety precaution. In case of unexpected machine malfunction, users might not be able to continue their experiments and have to reschedule. Affected reservations will be cancelled.
  • How can I retrieve my experimental data on BioCRF computers and how does BioCRF manage these data?
    Users can refer to our Data Download Guide for instructions. BioCRF does not use or back up users’ experimental data and we delete them periodically, users should download their files within 7 days.
  • How to acknowledge BioCRF in my work?
    With the proper acknowledgement of the use of our instruments and services in your publications (reports, presentations, papers, etc.) and grant applications, we get to measure our impact on the research community and assess if our resources are efficiently utilized. This metric is important for the continued funding and support of our operations and expansion - so that you could enjoy more high-quality instruments and services! ​ Any use of our resources should be acknowledged. Please acknowledge us as “Biosciences Central Research Facility, HKUST (Clear Water Bay)” in grant applications and the acknowledgement section of any publications.​ ​ Example: ​ We thank Biosciences Central Research Facility of HKUST (Clear Water Bay) to support the work in [flow cytometry/ histology/ general equipment/ genomics/ proteomics/ microscopy/ tissue culture*] core(s).​ *Please select the appropriate options Online form link:
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