AS Facility
Proteomics Mass Spectrometry Common Facility
Technical Director
Shu-Yu Lin +886-2-27855696,4012
Staff Scientist: Yi-Yun Chen +886-2-27855696,4019
MS Technicians: Ming-Chieh Tsai +886-2-27855696,4014
MS Technicians: Ronald Lin +886-2-27855696,4014

The centralized common mass spectrometry facilities located on the 4F at IBC includes a fleet of hybrid and Tribrid Orbitrap instruments configured primarily for advanced nanoLC-nanoESI-MS/MS analyses. At present, the Thermo LTQ-Orbitrap Velos and Elite systems are both used for routine proteomic ID and first screen analyses of less complex samples, while the high end Orbitrap Fusion and Lumos systems are the workhorses for advanced quantitative shotgun proteomics, PTMomics, glycoproteomics and glycomics. These are administered and operated under the Academia Sinica Common Mass Spectrometry Facilities for protein modification and proteomic analyses, the details of which including different modes of service and instrument bookings, and their respective charges can be found at The IBC facilities further house a Waters Synapt G2 HDMS configured with a fully automated hydrogen-deuterium exchange (HDX) system for protein structure and conformation analysis. Additional peptide and glycan mapping and sequencing are supported by a Sciex MALDI-TOF/TOF 5800 system. Interested new users are strongly advised to first contact the facility Manager and/or Technical Director to discuss research needs and workflow design from front end sample preparation to data analysis. Training courses, seminars and lectures are also on offer for potential users.

1. Thermo Orbitrap Velos Mass Spectrometer

The Thermo Scientific LTQ Orbitrap Velos combines the proven mass accuracy and ultra-high resolution of the Orbitrap mass analyzer, with the increased sensitivity and improved cycle time of the LTQ analyzer. Providing confidence of identification in complex samples.

Maximum Resolution: 100,000
Fragmentation method: CID, HCD

2. Thermo Orbitrap Elite Mass Spectrometer

Thermo Orbitrap Elite Mass Spectrometer combines a high-field Orbitrap mass analyzer and ion trap technology to deliver very high resolution, speed, sensitivity and complementary fragmentation information. It has parallel MS and MSn analyses capability which speeds analyses.

Maximum resolution: 240,000
Fragmentation method: CID, HCD, ETD

3. Thermo Orbitrap Fusion Tribrid Mass Spectrometer

The Thermo Scientific Orbitrap Fusion Tribrid Mass Spectrometer combines the best of quadrupole, ion trap and Orbitrap mass analysis in a revolutionary Tribrid architecture. The Tribrid structure allowed it to acquire CID, HCD, and ETD information with ion trap or Orbitrap detection at any level of MSn maximize flexibility for research applications. With Dynamic Scan Management further improves the maximum information able to acquire from samples.

Maximum resolution: 500,000
Fragmentation method: CID, HCD, ETD, EThcD

4. Thermo Orbitrap Fusion Lumos Tribrid Mass Spectrometer

Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer incorporates the brightest ion source, a segmented quadrupole mass filter with improved selectivity and ion transmission for improved ion transmission to the Orbitrap mass analyzer which provides ultra-high resolution for improved analytical result for experiments.

Maximum resolution: 500,000
Fragmentation method: CID, HCD, ETD, EThcD

5. Waters Synapt G2 High Definition Mass Spectrometer

Waters Synapt G2 is a high definition hybrid quadrupole/time-of-flight mass spectrometer. The ion mobility separation capability is used to separate different protein conformations and isomeric species. Additionally, it is coupled to a Waters HDX module to perform HDX experiment for protein dynamics and conformational changes.

Maximum Resolution: 40,000
Ion mobility separation
Waters hydrogen/deuterium exchange (HDX) module
Fragmentation method: CID, ETD

6. SCIEX 5800 TOF/TOF Tandem Mass Spectrometer

The TOF/TOF 5800 System has an unique OptiBeam On-axis Laser irradiation MALDI system that increases sensitivity in both MS and MS/MS modes over systems without an on-axis laser. With DynamicExit™ Algorithm, maximize the up-time and throughput of data acquisition.