Mass Spectrometry

The Multi User Mass Spectrometry Laboratory of the Department of Chemistry provides analytical services on a variety of mass spec platforms.

Open Access is granted to registered users for many of these instruments.  The lab manager provides additional support and guidance for more complex methodologies, instrumentation and data analysis.


LCQ Classic ion trap mass spectrometer (Thermofinnigan)

(Thermofinnigan, acquired in 1997 with funds from an NSF CRIF grant)

Access:  Open access
Ionization- electrospray
Mass analyzer- ion trap
m/z range - 150-2000
Mode of operation:  direct infusion
Note: Samples infused into the electrospray source must be of high purity, and without nonvolatile buffers or particulates that would clog the heated inlet. This mass spectrometer is discontinued with no manufacturer support.

JMS-600H High Resolution Mass Spectrometer (JEOL)

The JMS-600H is a compact double-focusing, high-resolution, magnetic sector mass spectrometer with resolving power of 25,000, using the 10% valley definition.  This instrument is used for accurate mass measurement of molecules.  Samples may be introduced into the ion source using a gas chromatograph (GC) or a direct insertion probe (DIP) and ionized by electron ionization (EI).  Polar and nonvolatile samples are usually introduced into the ion source by the FAB probe and ionized by fast atom bombardment (FAB).

Access:  Staff
Ionization:  FAB, EI, limited CI, DIP
Mode:  Positive
Mass Range:  HS Mode: 50- 800, HF Mode: 600-1800
Resolution: Generally set to 3000
Analyzer:  Magnetic and Electric Sectors
Software:  Shrader Software
LTQ linear ion trap mass spectrometer with Accela LC and PAL autosampler (Thermo)

(acquired in 2010 with funds from an HHMI Undergraduate Grant)

Access: Open
Ionization: ESI
Analyzer: linear ion trap
m/z range: generally 150-2000
MS/MS capability:  Yes
Software: XCalibur
The LTQ is equipped with an electrospray ionization source. It may be operated in direct infusion mode or interfaced with a liquid-chromatography (LC) system.
LCT Premier XE electrospray TOF mass spectrometer with UPLC (Waters)

(acquired in 2005 with funds from an NSF CRIF Grant)

The LCT Premier XE is a time-of-flight mass spectrometer equipped with an electrospray ionization source.  Instrument operation alternates between direct infusion mode and on-line LC-MS depending on lab and research needs.
Access: Open/Assisted
Ionization: ESI
Analyzer: TOF
m/z range: generally 150-2000
Resolution: 5,000 in V mode and 10,000 in W mode
Accurate Mass Capability: yes (staff only)
Mode:  direct infusion and UPLC-MS

Autoflex MALDI TOF/TOF (Bruker)

(acquired in 2016 with funds from DOW Foundation Grant)

The Autoflex is a state-of-the art matrix-assisted laser desorption ionization (MALDI) instrument used for analysis of mostly large synthetic and biopolymers.
Ionization: MALDI
Analyzer:  TOF
m/z range: generally 500 Da-120 kDa
Software: FlexControl and FlexAnalysis

Instrument Use Policy

With the exception of the magnetic sector instrument (JMS-600H), which is operated by lab personnel ONLY, the remaining mass spectrometers are available for individual use after training.

User Registration

All users must complete User Registration Form prior to training on the instrument(s) they plan to use.   A one-time training fee of $75 will be charged to your PTA.

Reserve Time

Trained users may book instrument time by signing the calendar for each mass spectrometer using the following web link:
If you need to use the instrument for more than two hours at one time you will need to consult the lab manager.

Mass Spec User List

Users of the lab are advised to subscribe to the mass spec user list to be alerted of instrument status and lab closures and changes to policies.

Lab Guidelines

Users must observe safe lab procedures.  Please notify lab personnel if there is any condition that prevents use of the instrument or endangers the safety of those present in the lab.

Users must sign into the logbook before beginning to work on the instrument and complete the time-of-use form after completion of their work.

All users must verify cleanliness of the instrument before and after running their own samples.  Work area must be left clear of debris including, used gloves, KimWipes, etc.

Lab entry is via keypad code.  This code will be shared at the discretion of the lab manager.

Users who intentionally or neglectfully misuse, damage, or contaminate the instruments and/or solvents will lose their privilege to use the instruments, and will be billed for any repairs, cleanup or decontamination.  This includes but is not limited to physical damage, chemical contamination, or corruption of the data systems.

Users are not to use the instrument control computers for SURFING on the web, playing games, downloading music, or emailing data.

Policy Regarding Preservation of Data

Lab personnel transfer data from instrument control computers to a local server (Seabiscuit) at intervals; the Seabicuit server is also mirrored onto a second disk.  Still, disk capacity is limited and ultimately even the data on the server have to be archived.  Users are thus asked to bring a flash drive with them to back up their data.  Each computer is connected to a router with multiple USB ports.  Please use these ports instead of the USB port on the computer.

Guidelines for Acknowledgement in Print

The CCE Multiuser Mass Spectrometry lab in Crellin B170 is a shared mass spectrometry laboratory. The mass spectrometers in this lab have been using funds from NSF (CRIF and MRSEC programs), Hughes Foundation, DOW, and CCE Division funds. Please acknowledge the lab in your publications to assist in acquisition of future funds needed to update its equipment.  Acknowledgement may be in this form:

"This research was enabled/benefited from the use of instrumentation made available by the Caltech CCE Multiuser Mass Spectrometry Laboratory."  Please email an electronic copy of any publication that made use of this lab's services.

FY 2020 Fees

Mass Spec Rates 2020

Please note that instrument time is charged on the basis of actual time used with a minimum visit time of 15
minutes and increments specific to each instrument. If you would like to use the facility and are external to Caltech, please contact either Mona Shahgoli at (626) 395-3372 or Naseem Troian at (626) 395-3378.


Mass Spectrometry Request Form

On-Campus User Registration Form

Facilities Use/Technical Services Agreement Form

Contact Information

Mona Shahgholi, Ph.D.
Telephone: (626) 395-3372

Mailing Address:
Chemistry 164-30
1200 East California Blvd
Pasadena, CA 91125