Mass spectrometers and preparation systems

These system are used for routine measurements of:

  1. Clumped isotopes of carbonate minerals and CO2 (Hagit Affek)

  2. Compound specific (e.g. DMS,  petroleum)  δ34S analysis at the picomole level by gas chromatography (GC) and high resolution multi-collector inductively-coupled plasma mass spectrometry (MC-ICP-MS) (Alon Amrani)

  3. Dust and soil phosphate δ18O  (Alon Angert)

  4. Organic δ13C and water δ18O (Eugenie Barkan

  5. Δ17O and δ18O of Oand H2O (Boaz Luz)

Computer cluster for modeling of atmospheric and oceanic Processes

The cluster comprises 192 Haswell i7 2.7GHz processors arranged in eight cores of 24 processors each, with each core containing 128GB. In addition, a separate 16-core, 512GB machine is available for big-data processing (Haim Garfunkel, Hezi Gildor).

Clean laboratory

The clean laboratory is used to prepare samples with pico- to nano molar levels of trace metals for concentration and isotopic composition analyses. Laboratory room surfaces are made of non-corrosive, acid resistant, metal free plastic materials (including floors, cabinets, and benches). It has a monitored positive pressure air supply with HEPA filtration, and has its own clean water supply. The laboratory is composed of several separated working spaces with different degrees of contamination-control, which serve different purposes.

Several analytical instruments, located in a next-door analytical laboratory, are used for the analysis of samples that were prepared in the clean laboratory.

Inductively Coupled Plasma Spectrometer (ICP-OES): Perkin Elemer Optima 3000 for major metal analysis.

Portable X-Ray Fluorescence Spectrometer (XRF): Bruker Tracer III-V/III-SD for qualitative determination of metals in solid samples.

Inductively Coupled Plasma Mass Spectrometer (ICP-MS): Agilent 7500cx for trace metal analysis.

High Resolution Multi Collector Inductively Coupled Plasma Mass Spectrometer (HR-MC-ICP-MS):  Neptune - Thermo for isotopic analysis of Pb, Sr, Nd, Fe, Mo, Cu, and Zn.  

 (Yigal Erel).

working in the clean lab

Magnetometer and shielded room

The magnetically shielded room is used for sensitive paleomagnetic experiments, and houses a fully automated superconducting rock magnetometer for magnetic measurements and characterization (Ron Shaar).

Electron Probe Micro-analyzer (EPMA)

electron probe

Omri Dvir   - Instrument supervisor

Electron Probe Microanalyzer (EPMA) Lab at the Hebrew University of Jerusalem,
Fredy and Nadine Department of Earth Science

In our lab, we have a JEOL Superprobe JXA-8230. SEMs are built mainly for imaging
samples using SEI or BSEI detectors. An EPMA is designed for chemical analysis of the
characteristic X-Rays emitted from a sample when probed by an electron beam. An
EPMA can quantify elemental concentration using electron dispersive spectroscopy
(EDS) and wavelength dispersive spectroscopy (WDS) to detect and count
characteristic X-Rays emitted from a sample. There are pros and cons to using the
EDS and WDS detector (mainly time and the necessity of experience using the
techniques). We will be happy to discuss these in person.

Imaging options in the EPMA:

-Back scattered electron imaging (BSEI) is sensitive to the mean electron density
(atomic weight). Back scattered electrons ate a form of elastic scattering in which
incoming incident electrons are bounced back off the sample to hit the detector.
(Electrons scattered by Coulombic interaction with the charge of the atomic nucleus
aka Rutherford scattering.)
-Secondary electron imaging (SEI) reveals the sample's topography due to the
variation in SE production at different tilt angles. Secondary electrons are ejected
from the k-shell by inelastic scattering interactions with the electron beam. They
originate within a few nanometers of the surface.
-Cathodoluminescence- Promotion of valence band electron to conducting band can
emit photon of electromagnetic radiation in the visible light region.

Chemical analysis in the EPMA:

-EDS Detector: Energy dispersive spectroscopy counts the number and energy of X-
Rays emitted from a specimen. The energy spectrum of the X-Rays characterizes the
atomic structure of the emitting element.
-WDS Detector: Wavelengthe dispersive spectroscopy counts the number of X-Rays
of a specific wavelength diffracted by a crystal. In contrast to EDS, WDS detectors
only count the X-Rays of a single wavelength at one time that characterize the
atomic structure of the emitting element.
For more information see the following website:


Atomic force microscope

The instrument is mainly used for studying water-rock interaction at the nano-scale. Nanomechanical properties and magnetic properties of geological materials are also routinely measured (Simon Emmanuel).

Confocal microscope

The microscope is used for live imaging of biomineralization in calcifying organisms (mainly foraminifera and corals), and allows imaging of fluorescence at a cellular level (Jonathan Erez).

Scanning Electron Microscopy (SEM)

Instrument supervisor: Omri Dvir    


The SEM can be used to examine surface details of solid materials. Internal surfaces

can be exposed by sectioning or fracturing. It is equipped with an energy dispersive

spectrometer which permits qualitative and quantitative compositional analysis.

Image analysis software permits detection, measurement and analysis of features of


  • Secondary electron imaging (morphology and surface topography)
  • Backscattered electron imaging (compositional contrast and phase distribution)
  • Digital image collection, enhancement and analysis
  • Elemental recognition and phase identification
  • Quantitative compositional analysis
  • Digital x-ray maps and linescans
  • Analysis of particle samples

JEOL JSM6400 Digital SEM with:

  • EDS (oxford) Energy Dispersive X-ray Analyzer