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Mass Spectrometry Resources at Caltech

CCE MultiUser Mass Spectrometry Lab

Manager: Mona Shahgholi,

Location: Crellin B170

Equipment can be operated by users after receiving proper training; service on submitted samples is also available.

Current MS instrumentation consists of:

  • JEOL Double focusing magnetic sector instrument with FAB and DIP/EI ionization for accurate mass measurement of submitted samples. This instrument is used primarily for analysis of small organics and organometallics (limited mass range ~1500 Da). (only submitted samples)
  • Applied BioSystems MALDI TOF spectrometer, used for mass analysis of larger MW molecules including polymers, oligonucleotides, oligosaccharides, and proteins/peptides. (This instrument will be replaced with a state-of-the art MALDI TOF from Bruker in Summer 2016.)
  • Thermo LCQ ion trap fitted with an electrospray ionization source, used for mass analysis of relatively polar and non-volatile molecules. This instrument is used extensively for mass analysis of synthetic organic and organometallic species that are not amenable to analysis by GC-MS. (The LCQ is completely discontinued by manufacturer with no service offered meaning that its projected lifetime depends on user care.)
  • Waters LCT electrospray TOF system for LC-MS with accurate mass analysis capability. The LCT is generally used for projects in need of LC-MS and accurate mass measurement.
  • Thermo LTQ ion trap electrospray system for LC tandem MS with nominal mass resolution. The LTQ is used for course instruction and various LC-MS projects.
  • Agilent MSD 5970 with 5890 GC- this is a very old instrument (>30 years), which is mainly used by lab personnel for screening purposes. The MSD is made available to student users ONLY when other GC-MS systems have failed.

Environmental Analysis Center

Director: Nathan Dalleska,

Location: Linde Laboratory

Equipment can be operated by users after receiving proper training; service on submitted samples is also available.

Current MS instrumentation consists of:

  1. Agilent 8800 ICP-MS. Tandem mass spectrometer capable of mass shifting reactions for interference removal. Sample introduction: pumped or self-aspirated nebulization of aqueous solutions, laser ablation (193 nm) of solids.
  2. Waters Xevo Q-TOF. High resolution (30,000 m/Δm), practical working mass range to 5,000 m/z. Electrospray and electrospray chemical Ionization. Sample Introduction: UPLC and infusion.
  3. Waters GCT-Premier. High resolution (7,000 m/Δm). Practical working mass range to 800 m/z. Electron Impact (EI) and Chemical Ionization (CI). Sample introduction by GC.
  4. Varian Saturn 2000 Ion Trap. MSn capable. EI and CI. CI using liquid reagents (e.g. methanol and acetonitrile). Unit mass resolution.
  5. HP (Agilent) 5972, 5973 MSDs. EI quadrupole mass spectrometers. Sample introduction via GC.

MS analysis capabilities by analyte type:

  • Small metabolites – GC-MS, UPLC-MS(-MS). Computational support for untargeted analyses including metabolomics and lipidomics.
  • Intact Polar Lipids – UPLC-MS(-MS).
  • Quantitative peptide analysis (if the project is not within the scope of the Proteome Exploration Laboratory—see below).
  • Permanent Gases – GC-MS.
  • C1 – C7 Hydrocarbons – GC-MS.
  • Organic mixtures for ID and quantitation – GC-MS(-MS)
  • Metal concentrations in aqueous solution – ICP-MS (from mg/L to ng/L). Most elements but not H, He, C, N, O, F, or Ar.

Beckman Institute Proteome Exploration Lab

Manager: Tsui-Fen Chou,

Location: Beckman Institute 201


The PEL performs state-of-the-art research in proteomics-based mass spectrometry, in collaborative mode for major users or on a fee-for-service basis for occasional users. The lab is currently equipped with an Agilent 1100 MSD instrument, two Thermo EASY-nLC Orbitrap instruments (Classic and Elite), a Thermo Easy nLC Q-Exactive, a Thermo Easy nLC Fusion and an AB Sciex nanoLC QTRAP. Our instruments have collision induced dissociation (CID), high energy collision induced dissociation (HCD) and electron transfer dissociation (ETD) capabilities. Ancillary instrumentation includes a Nanomate direct infusion device, additional HPLC systems, capillary puller etc. Our bioinformatics suite contains a Mascot server, MaxQuant, the TransProteomics Pipeline, Scaffold, Sequest, ROCCIT and other in-house developed software tools that are constantly being developed.

Caltech Center for Catalysis and Chemical Synthesis

Manager: Scott Virgil,

Location: Schlinger 301A

The 3CS includes several GC-MS and LC-MS instruments for versatile analysis of reaction outcomes:

Agilent 5975C GC-MS

Agilent G1946 LC-MS (1500 m/e)

Agilent G6140 UHPLC-MS (1350 m/e)

Agilent G6220 TOF LC-MS

Caltech Microanalytical Center

Manager: Yunbin Guan,

Location: Arms Subbasement


The Microanalytical Center houses two Secondary Ion Mass Spectrometry (SIMS) instruments, also known as ion microprobes. The Cameca NanoSIMS 50L is a type of ion microprobe designed for elemental and isotopic analysis of ultra-fine features (with spatial resolutions down to ~50 nm). It also offers extremely high sensitivity at high mass resolution and the capability of simultaneously measuring up to seven masses from the same small volume. The Cameca IMS 7f-GEO is a magnetic sector SIMS instrument based on the Cameca IMS 7f, but modified for geoscience applications. The combination of these two state-of-the-art ion microprobes in one laboratory provides powerful diverse capabilities in trace and isotope analysis, depth profiling, ion imaging and geochronology, with low detection limits, high spatial resolution, and/or high precisions.

Research Groups with Specialized MS Capabilities

Advanced Isotopic Analysis

PI John Eiler,

This group operates a number of instruments for high-resolution studies of isotope distribution, including detailed analysis of multiply-substituted isotopologues of light hydrocarbons, rare gases, biological and mineralogical samples, and measurements of site-specific isotopic distributions. Some of the instruments in the lab include: Thermo Fisher IRMS 253 Ultra (the prototype, and a second to arrive at the end of this year), DFS, Q Exactive GC, and several lower resolution gas source IRMS instruments. Most of these machines are modified in significant ways for natural abundance stable isotope measurements.