A

The Stanford–U.S. Geological Survey SHRIMP Ion Microprobe—

A Tool for Micro-Scale Chemical and Isotopic Analysis

nswers to many questions in 

Earth science require chemical 

analysis of minute volumes of minerals, 

volcanic glass, or biological materials. 

Secondary Ion Mass Spectrometry 

(SIMS) is an extremely sensitive 

analytical method in which a 5–30 

micrometer diameter “primary” beam of 

charged particles (ions) is focused on 

a region of a solid specimen to sputter 

secondary ions from 1–5 nanograms 

of the sample under high vacuum. The 

elemental abundances and isotopic 

ratios of these secondary ions are 

determined with a mass spectrometer. 

These results can be used for 

geochronology to determine the age 

of a region within a crystal thousands 

to billions of years old or to precisely 

measure trace abundances of chemical 

elements at concentrations as low as 

parts per billion. A partnership of the 

U.S. Geological Survey and the Stanford 

University School of Earth Sciences 

operates a large SIMS instrument, 

the Sensitive High-Resolution Ion 

Microprobe with Reverse Geometry

(SHRIMP–RG) on the Stanford campus.

The Stanford-USGS SHRIMP–RG in the room constructed specifically for the instrument in the 

basement of the Green Earth Sciences Research Building, Stanford University. Control console 

is at right, behind two black computer monitors. Specimen chamber is at extreme right, behind 

the control console. The primary ion source is out of view behind the specimen chamber. 

Secondary ions sputtered from the specimen move from right to left through the doubly focusing 

mass spectrometer, which is maintained at high vacuum. The white “SHRIMP RG” object in the 

center of the image is the laminated electromagnet of the 1-m-radius magnetic sector. The large 

curved stainless steel box left of the magnet is the electrostatic analyzer of the 1.2-m-radius 

electrostatic sector. Mass- and energy-selected secondary ions are counted by an electron 

multiplier in the cylindrical device in the lower left foreground.

Big Machines to Study Tiny Things

The need to be able to separate a rare isotope from a nearby mass (abundance sensitivity) in a small sample and ability to resolve 

very small differences in mass in geoscience 

research have led to the development of large 

Secondary Ion Mass Spectrometry (SIMS) 

instruments. In geoscience labs around the 

world there are now approximately 30 such 

machines, with about equal numbers of 

Australian-made SHRIMP and French-made 

CAMECA ion probes. Housed in the Stanford 

University School of Earth Sciences, the joint 

Stanford-U.S. Geological Survey (USGS) Ion 

Microprobe Laboratory operates a SHRIMP–

RG that is one of two in which the electrostatic analyzer is positioned downstream of 

the 1-m-radius magnetic sector of the doubly 

focusing secondary ion mass spectrometer. 

This reverse geometry (RG) enables precise 

analysis at very high mass resolving power. 

Specimens are sectioned and polished grains 

cast in epoxy resin, natural grain surfaces 

positioned parallel to the mount surface by 

pressing grains into soft indium metal, or 

polished thin sections of rocks. Optical and 

scanning electron microscope (SEM) images 

are used to map and characterize the material 

to be analyzed. Specimens are coated with a 

thin layer of electrically conductive material 

such as gold to prevent charge build-up from 

the primary ion beam. Inside the high vacuum 

Specimen mount for the SHRIMP–RG with mineral 

grains embedded in epoxy resin, then ground and 

polished to expose interiors for analysis. The 1-inchdiameter disk has been coated with a thin layer of 

gold that conducts electricity.

S T A N F O R D U N I V E R S I T Y

SCHOOL OF EARTH SCIENCES

E A R T H · E N E R G Y · E N V I R O M E N T

U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2012-3067

May 2012
Uranium–Lead Geochronology of Zircon

Zircon crystal from andesite erupted from Redoubt 

Volcano, Alaska. Zircon was mounted in epoxy 

resin, ground and polished to expose interior, and 

imaged with a scanning electron microscope (SEM). 

Internal compositional variation is revealed by 

cathodoluminescence (CL), in which light emitted 

under electron bombardment is proportional to the 

amount of chemical impurities (trace elements) in 

the crystal. White ellipses indicate spots analyzed by 

SHRIMP–RG for uranium-lead (U–Pb) geochronology. 

Ages are given in millions of years before present 

(Ma). Truncated CL banding in the upper right 

indicates that the older part of the crystal is a 

fragment of ancient zircon, while the more uniform 

CL in the lower left is a much younger overgrowth. 

Although recovered from a young volcanic deposit, 

this zircon crystal formed in rock beneath the volcano 

and gives unique information on the geologic history 

of the Alaska Peninsula. Scale bar is 50 micrometers 

(μm) long. After Bacon and others (2012), figure 4B.

Uranium–Lead Ages of Detrital Zircons

Single-grain detrital zircon uranium-lead (U–Pb) 

ages, plotted as histograms (pale blue) and as 

probability density distributions (“age spectra,” 

red curves), for three samples of metamorphosed 

sandstone from the Franciscan Complex of 

northern California, which was accreted to 

the continent by Cretaceous subduction of the 

Farallon Plate. The maximum depositional age 

of each sandstone is given by the youngest 

zircons (for example, Dep Age ≤123 Ma). Vertical 

dashed blue lines are maximum depositional 

ages from youngest dated zircon for Valentine 

Spring Formation (VSF) and Yolla Bolly Terrane 

(YBT). Major age peaks reflect sources within 

the Sierra Nevada magmatic arc. Modified after 

figures 5d–f of Dumitru and others (2010).

SHRIMP–RG, samples are manipulated by 

a digitally encoded mechanical stage that 

automatically drives to analysis locations on 

the specimen that are preselected by the scientist. During an analysis, the primary beam 

sputters a few atomic layers per second from 

the specimen in a 5–30 micrometer diameter 

spot. About 1–5 nanograms of material are 

removed during a typical 10–20 minute analysis. Very high resolving power for different 

masses is required because certain secondary 

ions produced during sputtering may interfere 

with the ions of interest. The SHRIMP–RG is 

capable of separating two adjacent masses by 

an amount (0.005 to 0.03 atomic mass units, 

depending upon mass range) that is sufficient 

for most applications without reducing the 

secondary ion beam intensity. Ion arrivals are 

detected at the end of the mass spectrometer 

by a sensitive counting system and converted 

to isotope ratios or elemental concentrations 

by comparison with similar measurements 

on reference materials (standards) of known 

composition. Development of new analytical 

techniques often demands identification and 

characterization of new standards.

A Government–Academic Partnership

The SHRIMP–RG at the Stanford-USGS 

Ion Microprobe Laboratory is the centerpiece of the Stanford-USGS Micro Analysis 

Center (SUMAC). SUMAC was initiated in 

the 1990’s, and the SHRIMP has been operational since 1998. Scientists from USGS 

offices around the country visit the laboratory 

to analyze specimens in research supported 

by Mineral Resources, Geologic Mapping, 

Volcano Hazards, Climate, and other Geological Survey programs. Within USGS, 

the lab is organizationally housed under the 

Associate Director for Energy and Minerals, 

and Environmental Health Mission Area. On 

the Stanford side, faculty, students, and other 

researchers use the SHRIMP–RG for a wide 

variety of investigations. External researchers from within the United States and other 

countries also have access to the laboratory. 

External investigators pay a standard daily 

fee for analysis time; Stanford and USGS 

scientists pay a reduced daily fee that reflects 

the investment of the two organizations. 

Although most external researchers are U.S. 

academics supported by the National Science 

Foundation, others have come from Canada, 

China, Taiwan, the United Kingdom, Israel, 

Russia, Brazil, and New Zealand. Research 

by these visiting scientists fosters innovative 

science, complements USGS and Stanford research programs, and builds the international 

reputation of the lab. To staff the lab, Stanford 

and USGS supply Co-Directors, Staff Scientists, and student assistants. An electronics 

technician is contributed by USGS, and space 

in the Green Earth Science Research Building 

is provided by Stanford. Income from fees 

covers spare parts and supplies, modifications 

to the SHRIMP–RG to improve performance, 

and partial salary support for a staff scientist.

Geochronology

The Stanford-USGS SHRIMP–RG has 

been intensely used for uranium-lead (U–Pb) 

geochronology since the instrument was 

installed in 1998. This versatile method exploits the slow radioactive decay of parent U 

isotopes to daughter Pb isotopes as a natural 

clock for the time elapsed since crystallization 

of the material analyzed, from as little as a 

few hundred thousand years to zircons 4.5 

billion years old recovered from meteorites. 

Uranium is present at tens to thousands of 

parts per million (ppm) as a trace constituent 

in some natural materials. Zircon is widely 

used to date crystallization of igneous rocks 

and to provide ages of grains in sediments. 

Less commonly, other “accessory” minerals, 

such as monazite and titanite (sphene), are 

dated by U–Pb. Geological applications include determining ages of granite and other 

types of plutonic rock bodies, volcanic ash 

beds, metamorphic recrystallization of rocks, 

and formation of metallic ore deposits, as 

well as ages of individual sand grains that 

have been deposited by water and wind. The 

SHRIMP–RG’s high mass-resolving power 

allows key trace element concentrations in 

accessory minerals to be determined in rou-
tine U–Pb geochronology sessions, “fingerprinting” compositional populations and revealing origins of these minerals. The useful 

range of geochronology with the SHRIMP–

RG is extended to the recent past (less than a 

few hundred thousand years) by uranium-series disequilibrium dating, in which 238U and 

geologically short-lived U and thorium (Th) 

daughter products in the decay chain (234U, 230Th) are measured to determine the time 

since disturbance of a geochemical system, 

such as precipitation of silica (SiO2

) from 

groundwater onto rock surfaces or growth 

of zircon in magma erupted from a volcano. 

Dating hydrogenic silica (opal) by SIMS was 

developed at SUMAC, where new methods 

are constantly under investigation—recently 

U-series geochronology of igneous accessory minerals allanite and chevkinite.

Trace Element Geochemistry

In sessions devoted to measurement of 

elemental concentrations, most of the periodic table of elements is accessible with the 

SHRIMP–RG for abundances from parts 

per million (ppm) to parts per billion (ppb). 

Because secondary ion yield varies with the 

kind of material being analyzed (known as 

the matrix effect), the laboratory has developed a set of mineral and glass standards 

for accurate calibration of trace element 

concentrations. Concentrations of many 

trace elements from lithium (atomic number 3) to uranium (atomic number 92) may 

be determined in a single analytical routine 

for several common minerals and volcanic 

glass. Many specialized applications have 

been pursued with the SHRIMP–RG. Crystallization temperatures of zircon, quartz, 

titanite, and rutile are revealed by analysis 

of trace amounts of titanium in zircon and 

quartz and of zirconium in titanite and rutile, using recently published calibrations of 

the temperature dependence of these concentrations in minerals. The natural glass 

particles in volcanic ash beds can be “fingerprinted” by trace element concentrations 

and these then used to match ash samples 

from widely separated localities. Additionally, trace element concentrations in minerals can be used, again through published 

calibrations, to infer chemical compositions 

of magma or fluid in which the crystals 

grew. Concentrations of “volatiles,” such as 

water, carbon dioxide, sulfur, fluorine, and 

chlorine, dissolved in volcanic glass droplets trapped in crystals (“melt inclusions”) 

give invaluable information on magma 

properties and can yield the depth at which 

magma resided before a volcanic eruption. 

Isotopes and Trace Elements in 

Biological Materials

In research employing the SHRIMP–RG 

on biological calcium carbonate, such as 

coral, mollusc shells, and ear stones of fish 

(otoliths), trace concentrations of certain 

elements indicate the salinity and composition of the water in which the animal lived. 

In some cases, trace elements have been 

used not only to infer water chemistry but 

also temperature, such as in coral. One early 

SHRIMP–RG study measured isotopic 

ratios of strontium (87Sr/86Sr) in salmon otoliths, which grow in daily increments, to determine migration histories of juvenile fish. 

50 μm

> 550

520-550

420-460

500-520

480-500

460-480

Qtz (M)

Kfs

Bt

Ms (S)

Ms (M)

Qtz (S)

Pl

Growth 

temperature 

in °C

Geological “Thermometry”

Scanning electron microscope (SEM) image 

of polished thin section of a metamorphosed 

(recrystallized) sedimentary rock from the 

Peninsular Ranges of southern California. 

In this backscattered-electron (BSE) image, 

brightness is proportional to the average 

atomic number of the material; that is, 

minerals rich in iron (Fe, atomic number 

26) are brightest and minerals rich in silica 

(SiO2, atomic numbers 14 and 8) are darkest. 

This specimen illustrates progressive 

textural development of muscovite (Ms) 

+ quartz (Qtz) symplectite and quartz + 

plagioclase (Pl) myrmekite (types of mineral 

intergrowths) in response to changing 

temperature during metamorphism. M, 

matrix; S, symplectite; Bt, biotite; Kfs, 

potassium feldspar. Circles indicate both 

location and size of ion beam spots. Colors 

indicate temperatures during mineral growth 

calculated from trace titanium concentration 

in quartz. Scale bar in upper left is 50 

micrometers (μm) long. After Peterman and 

Grove (2010, figure 2B).

Uranium-Series Geochronology of 

Opaline Silica

False-color cathodoluminesence image of 

the tip of a secondary hydrogenic calcite 

blade from the deep vadose zone at Yucca 

Mountain, Nevada, showing growth 

layering in opal (orange) and calcite 

(blue). Circles show locations of spots 

analyzed for uranium-series (U-series) 

dating along with ages, in thousands of 

years (ka), for bright, U-rich layers that 

formed during drier interglacial periods. 

Black lines drawn along growth surfaces 

in calcite correlate opal layers with 

similar U concentrations and ages. The 

average mineral growth rate of ~ 1.54 μm/

ky for opal in the upper central part of 

the image remained uniform over at least 

the past 300 ky despite large climatecontrolled fluctuations in effective surface 

moisture. After graphical abstract from 

Paces and others (2011), with permission 

from Elsevier.
Charles R. Bacon1

, Marty Grove2,

Jorge A. Vazquez3

, and Matthew A. Coble4

1

SUMAC Co-Director, U.S. Geological Survey

2

SUMAC Co-Director, Stanford University

3

Staff Scientist, U.S. Geological Survey

4

Staff Scientist, Stanford University

Edited by Peter H. Stauffer

Graphic design by Judy Weathers

Any use of trade, product, or firm names is for 

descriptive purposes only and does not imply 

endorsement by the U.S. Government.

For more information contact:

Charles R. Bacon

U.S. Geological Survey, MS 910

345 Middlefield Road

Menlo Park, CA 94025

Tel. (650) 329-5246

cbacon@usgs.gov

or

Marty Grove

Department of Geological and

Environmental Sciences

Stanford University

Stanford, CA 94305

Tel. (650) 721-5490

mjgrove@stanford.edu

http://shrimprg.stanford.edu

This Fact Sheet and any updates to it are available 

online at http://pubs.usgs.gov/fs/2012/3067/.

Future Science at SUMAC

Advancing geochronology across a broad 

spectrum of geological environments will 

continue to be a principal occupation of the 

Stanford-USGS SHRIMP–RG. Similarly, 

types of trace element concentration measurements will expand. SUMAC encourages new 

applications of the SHRIMP–RG for which it 

can be a useful tool. In U–Th–Pb geochronology and for many trace element applications, 

the SHRIMP–RG uses a negatively charged 

oxygen ion primary beam to yield positively 

charged secondary ions to the mass spectrometer. In 2012, a major investment in new 

equipment will greatly facilitate use of the 

SHRIMP–RG for analysis of elements such 

as carbon and sulfur that are most efficiently 

measured as negatively charged secondary 

ions produced by sputtering with a positively 

charged cesium ion primary beam.

A Selection of Recent Publications 

Featuring Data From the StanfordUSGS SHRIMP–RG

 For a complete bibliography of more than 350 

citations, visit http://shrimprg.stanford.edu. 

Bacon, C.R., Vazquez, J.A., and Wooden, J.L., 

2012, Peninsular terrane basement ages 

recorded by Paleozoic and Paleoproterozoic 

zircon in gabbro xenoliths and andesite from 

Redoubt Volcano, Alaska: Geological Society of America Bulletin, v. 124, p. 24–34.

Barth, A.P., Wooden, J.L., Coleman, D.S., and 

Vogel, M.B., 2009, Assembling and disassembling California; A zircon and monazite 

geochronologic framework for Proterozoic 

crustal evolution in southern California: 

Journal of Geology, v. 117, 221–239.

Sediment Provenance and Sedimentary Rocks

Dumitru, T.A., Wakabayashi, J., Wright, J.E., 

and Wooden, J.L., 2010, Early Cretaceous 

(ca. 123 Ma) transition from nonaccretionary behavior to strongly accretionary 

behavior within the Franciscan subduction complex: Tectonics, v. 29, TC5001, 

doi:10.1029/2009TC002542.

Egger, A.E., Colgan, J.P., and York, C., 2009, 

Provenance and palaeogeographic implications of Eocene–Oligocene sedimentary rocks 

in the northwestern Basin and Range: International Geology Review, v. 51, p. 900–919.

Paleohydrology and Paleoclimate

Maher, K., Wooden, J.L., Paces, J.B., and 

Miller, D.M., 2007, 230Th/U dating of surficial 

deposits using the ion microprobe (SHRIMPRG); a microstratigraphic perspective: Quaternary International, v. 166, p. 15-28.

Paces, J.B., Neymark, L.A., Whelan, J.F., 

Wooden, J.L., Lund, S.P., and Marshall, 

B.D., 2010, Limited hydrologic response to 

Pleistocene climate change in deep vadose 

zones — Yucca Mountain, Nevada: Earth and 

Planetary Science Letters, v. 300, p. 287–298.

Mineral Crystallization Temperatures

Grujic, D., Stipp, M., and Wooden, J.L., 

2011, Thermometry of quartz mylonites; 

Importance of dynamic recrystallization on 

Ti-in-quartz re-equilibration: Geochemistry, 

Geophysics, Geosystems, v. 12, Q06012, 

doi:10.1029/2010GC003368.

Peterman, E.M., and Grove, M., 2010, Growth 

conditions of symplectic muscovite + 

quartz; Implications for quantifying retrograde metamorphism in exhumed magmatic 

arcs: Geology v. 38, p. 1071–1074.

Mineral Resources

Vikre, P., Browne, Q.J., Fleck, R., Hofstra. A., 

and Wooden, J., 2011, Ages and sources of 

components of Zn–Pb, Cu, precious metal, 

and platinum group element deposits in 

the Goodsprings District, Clark County, 

Nevada: Economic Geology, v. 106, p. 

381–412.

Winter, L.S., Tosdal, R.M., Mortensen, J.K., 

and Franklin, J.M., 2010, Volcanic stratigraphy and geochronology of the Cretaceous 

Lancones Basin, northwestern Peru; Position and Timing of VMS: Economic Geology, v. 105, p. 713–742.

Geochronology and Geochemistry of 

Igneous Rocks

Barth, A.P., and Wooden, J.L., 2010, Coupled 

elemental and isotopic analyses of polygenetic zircons from granitic rocks by ion 

microprobe, with implications for melt evolution and the sources of granitic magmas: 

Chemical Geology, v. 277, p. 149–159.

du Bray, E.A., Bacon, C.R., John, D.A., 

Wooden, J.L., and Mazdab, F.K., 2011, 

Episodic intrusion, internal differentiation, 

and hydrothermal alteration of the Miocene 

Tatoosh intrusive suite south of Mount 

Rainier, Washington: Geological Society of 

America Bulletin, v. 123, p. 534–561.

Magma Evolution Beneath Volcanoes

Carley, T.L., Miller, C.F., Wooden, J.L., Bindeman, I.N., and Barth, A.P., 2011, Zircon from 

historic eruptions in Iceland; Reconstructing 

storage and evolution of silicic magmas: Mineralogy and Petrology, v. 102, p. 135–161.

Claiborne, L.L., Miller, C.F., Flanagan, D.M., 

Clynne, M.A., and Wooden, J.L., 2010, 

Zircon reveals protracted magma storage and 

recycling beneath Mount St. Helens: Geology, v. 38, p. 1011–1014.

Wilson, C.J.N., and Charlier, B.L.A., 2009, Rapid 

rates of magma generation at contemporaneous 

magma systems, Taupo volcano, New Zealand; 

insights from U–Th model-age spectra in zircons: Journal of Petrology, v. 50, p. 875–907.

The Stanford-USGS SHRIMP–RG is housed 

in the basement of the Green Earth Sciences 

Research Building at Stanford University. Regional Geology and Tectonics