Mass Spectropmetry Resources at Caltech

This page summarizes mass spectrometry capabilities available to the Caltech research community. Interested users are highly encouraged to contact people in charge BEFORE starting their experiments to maximize success in their experiments.

Suggestions for improving or adding to this listing are most welcome; please send them to Jay Labinger, BI Administrator, at

Service Facilities

1. 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:
1. 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)
2. 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.)
3. 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.)
4. 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.
5. 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.
6. 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.

2. Environmental Analysis Center

Manager: Nathan Dalleska,
Location: Linde+Robinson Lab

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:
1. Small metabolites – GC-MS, UPLC-MS(-MS). Computational support for untargeted analyses including metabolomics and lipidomics.
2. Intact Polar Lipids – UPLC-MS(-MS).
3. Quantitative peptide analysis (if the project is not within the scope of the Proteome Exploration Laboratory—see below).
4. Permanent Gases – GC-MS.
5. C1 – C7 Hydrocarbons – GC-MS.
6. Organic mixtures for ID and quantitation – GC-MS(-MS)
7. 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.

3. 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.

4. 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

5. 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

1. Innovative Applications of Mass Spectrometry

PI Jack Beauchamp,
The overall objective of research in Innovative Applications of Mass Spectrometry is the opportunistic development of novel mass spectrometric instruments and experimental methodologies that have specific applications to chemical, biochemical, environmental, and space science problems, and to assist members of the Caltech and JPL community in developing new methods for chemical analysis. Collaborations to develop new instruments and methods involving mass spectrometry are encouraged.

Instrumentation includes:
1. Waters Q-TOF-II quadrupole time of flight mass spectrometer. This recently added instrument has moderately high mass resolution (15,000 and rapid scanning capability compared to the ion trap and ICR instruments). In addition to routine MS analysis it is being adapted for atmospheric pressure chemical imaging studies.
2. Thermo LCQ Deca XP ion trap mass spectrometer. This instrument is used for routine applications utilizing electrospray ionization. This instrument is also used in undergraduate laboratories to introduce students to mass spectrometry.
3. LTQ-XL Thermo Linear Ion Trap. The LTQ instrument provides approximately 10X sensitivity and unit mass resolution or better up to m/z 4,000 amu, facilitating, for example, the study of protein complexes using ESI. This instrument is used for development and applications of reagents for proteomics and glycomics. (For high resolution mass spectrometry (exact mass measurements) we recommend use of the LTQ-FT and LTQ-Orbitrap instruments in the PEL (see above).
4. LTQ-XL Thermo Linear Ion Trap. This instrument has several ion sources for different types of experiments, including ESI, AP-MALDI, desorption electrospray ionization (DESI), Direct analysis in real time (DART), field induced droplet ionization (FIDI), and, most recently, an atmospheric pressure ion mobility spectrometer (IMS) to allow simultaneous analysis of the shapes and molecular weights of ionic species.
5. Reflectron time of flight mass spectrometer. This is a research TOF mass spectrometer with dual detectors, optical windows with access to the sample and ion turn around point in the reflectron (for multiple laser ionization and ion photodissociation studies). This instrument is currently being used to develop new methods for rapid DNA sequencing and for selective ionization and detection of phosphorylated peptides as well as a test bed for joint Caltech/JPL development of a high performance mass spectrometer for in situ studies in space environments, specifically Titan.
6. Corsair orthogonal sampling time of flight mass spectrometer (Analytica of Branford). This instrument has a dual inlet ESI source that can be removed to accommodate any atmospheric pressure ion source. Currently we have an ion funnel attached to the inlet that operates at Martian surface ambient pressure to evaluate the viability of experimental methodology for future flight instruments (collaboration with JPL). Two additional instruments have been acquired and are available for future collaborative research projects.

Additional instruments include a quadrupole mass spectrometer equipped with an ESI ion source and several ion mobility spectrometers, one of which has now been interfaced to the LTQ ion trap MS (#4 above).

2. 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.