ToF SIMS – Time of Flight Secondary Ion Mass Spectrometry

What is ToF SIMS? What is it used for, and what sort of information can it provide? Which samples are suitable (and which are not)? In this series, we will answer all these questions and more.

Time-of-Flight Secondary Ion Mass Spectrometry (ToF SIMS) is a surface analysis technique used to study the chemical composition of solid surfaces and thin films in three dimensions.

Illustration describing ToF SIMS

A focused beam of primary ions bombards a target surface, creating a plume of neutral atoms/molecules, secondary ions, and electrons. The secondary ions are collected and analysed using a time-of-flight mass spectrometer. The mass spectrometer measures an ion’s mass-to-charge ratio (m/z) by precisely timing how long it takes to reach the detector – the “time of flight”.

By scanning the primary ion beam across an area of the sample, a chemical map of the surface is formed pixel by pixel. Scientists and technicians use ToF SIMS daily for fundamental research, routine analysis, and quality control in academic and industrial settings.

For many years, the limitations of the primary ion beam confined the analysis to looking at atomic species and small molecules. With advances in instrument and ion beam design, modern instruments such as the J105 SIMS are now routinely imaging large intact molecules. These new capabilities have caused an explosion in new applications, and more papers are published each year in bio and bio-related fields using ToF SIMS.

Anatomy of a ToF SIMS instrument

ToF SIMS instruments are often larger and more expensive than most other analytical instruments found in a lab. High-vacuum conditions (< 1×10-6 mbar) are required to prevent ions from colliding with gas molecules in the air, requiring bigger vacuum pumps, more robust seals, and additional precautions to prevent leaks.

Graphic showing the operation of the J105 SIMS instrument from Ionoptika.
Operation of the J105 SIMS ToF SIMS instrument. 1. The ion beam bombards the sample releasing secondary ions, electrons, and neutrals. 2. The secondary ions are collected. 3. Secondary ions are cooled and focused into the mass spectrometer. 4. The mass spectrometer records the flight time of the ions and converts this to a mass spectrum.
Primary componentsSecondary components
Sample analysis chamber (SAC)Sample introduction System
Primary ion beamCryogenic cooling for low-temperature analysis
Secondary ion extraction opticsCharge compensation, e.g., electron beam
Mass spectrometerSecondary electron imaging

Key Benefits of ToF SIMS

  • Spatial resolution. ToF SIMS achieves significantly higher spatial resolutions than other imaging methods, thanks to beam sizes as small as a few hundred nanometres.
  • Speed. The time-of-flight mass spectrometer operates at much higher rates than other MS techniques. ToF SIMS instruments can run at speeds up to 1000 pixels per second.
  • 3D imaging. The primary ion beam removes a small amount of material each time it scans across the surface. By making multiple passes over the same area, a 3D map of the material builds up layer by layer.
  • Sensitivity. Small spot sizes and shallow impact craters result in tiny analysis volumes, which require great care to prevent signal loss. As a result, SIMS is generally more sensitive than other forms of mass spectrometry.
  • Dynamic range. The ions in a ToF SIMS spectrum can range from a single hydrogen ion to intact protein molecules several thousand daltons in size.
  • Applications. The breadth of applications for ToF SIMS is enormous, ranging from metallurgy to fundamental biology and most things in-between.

Applications of ToF SIMS

ToF SIMS provides a detailed three-dimensional chemical map of a sample. Information about the atoms and molecules that make up the sample, their distribution, and any contamination present are all revealed. This type of information is beneficial for many applications.

Academic research labs, industrial quality control, and research organisations use ToF SIMS daily. Disciplines as diverse as materials science, analytical chemistry, biology, geology, pharmaceutical science, and many others benefit from the detailed chemical information ToF SIMS provides.

2D Imaging

2D images are the most common mode of operation for ToF SIMS applications, whereby the ion beam scans the surface, acquiring a mass spectrum at each pixel. The image resolution can vary from a few hundred pixels to over four million.

Images of individual mass channels show the precise distribution of ions across the field of view. Overlaying multiple mass channels can show the distribution of different ions and how they relate to each other.

The image below shows three individual ion images and an overlay image representing different components of a biological tissue sample.

ToF SIMS image of a rat cerebellum


Analysis of a ToF SIMS spectrum provides information on the atomic or molecular makeup of the sample and can inform about the general abundance of various compounds. It is also possible to determine atomic ratios in some cases, but this requires well-controlled samples and careful use of reference materials.

Tandem mass spectrometry is a feature on most major ToF SIMS instruments and is extremely useful for confidently identifying ions. Tandem MS, also known as MS/MS, or MS2, involves isolating a secondary ion of interest, fragmenting it, and collecting the resulting fragments in a mass spectrum. By analysing the daughter peaks, it is possible to determine the parent ion with a high level of precision.

MS/MS spectrum of the phospholipid PC34:1+K acquired on the J105 SIMS instrument.
A Tandem MS spectrum of a phospholipid species in a tissue sample acquired on the J105 SIMS instrument. Analysing the fragment pattern confirms the identity of the parent ion as PC34:1+K.

Depth profiling

A powerful analysis mode, depth profiling involves etching vertically through the sample and acquiring a mass spectrum at every layer. The result is a profile of all atoms/molecules through the sampled volume. Large cluster ions reduce damage to sub-surface layers, minimising interlayer mixing and maximising depth resolution. With the right ion beam and sample combination, depth resolution as low as a few nanometres is possible.

Depth profile through the NIST Ni/Cr standard reference material using a C60 beam.

Depth profile through the NIST Ni/Cr standard reference material using a C60 beam, showing 5 nm depth resolution.

3D Imaging

The feature that sets ToF SIMS apart from other mass spectrometry and analytical techniques is the ability to acquire 3D data sets. Like a depth profile, a 3D analysis involves acquiring many 2D layers repeatedly over the same area, etching material with each pass, and building up a three-dimensional view of the sample. Large cluster ions are ideal for 3D analysis as they produce very little damage and can therefore be used to etch and analyse the sample simultaneously.

Unlike techniques like AFM, which capture the 3D topography of the sample, SIMS cannot distinguish 3D objects from flat objects. The technique works best for flat samples with layers of interest below the surface, as in the OLED example below. It is possible to reconstruct the topography of a non-flat sample; however, this requires prior knowledge of the material structure. 

3D ToF SIMS image of an OLED screen, showing the different components of each sub-pixel unit.
This 3D ToF SIMS image of an OLED screen is acquired on the J105 SIMS using a 70kV water cluster primary ion beam. The RGB subpixel units appear at different distances from the surface, depending on their colour.

Read more about the applications of ToF SIMS in our Application Notes section. Or, to dive deeper into more advanced topics, check out the list of publications using our equipment here. You might also like to learn more about how the J105 SIMS operates, which you can read here.

How the J105 SIMS works: An introductory guide

The J105 SIMS is a state-of-the-art 3D imaging ToF SIMS combining innovative design with cutting-edge science that has redefined ToF SIMS. Designed to exploit the benefits of cluster ion beams, the J105 delivers exceptional sensitivity to molecular ions, 3D MS imaging, and consistent performance across all samples.

In this article, we aim to give you an overview of how the J105 SIMS works, as it is quite different to other ToF SIMS. We will guide you through the various features of the instrument and explain their purpose, how they work, and what the benefits are.

How the J105 SIMS works: an introductory guide

1.      The Ion Beam

The J105 was designed to get around many of the limitations faced by traditional ToF SIMS instruments, particularly for biological samples. One of the ways this is achieved is by not pulsing the primary ion beam, but instead running it in DC, or continuous mode. This is a major advantage and is what makes the J105 a very different instrument to most other ToF SIMS.

One of the biggest advantages of having a continuous beam is that any ion beam, no matter what size, can be used as the primary source. This gives the user a lot of choice when designing their experiment. We’ll cover the intricacies of different ion beams in a different article, but for the purposes of this discussion we’ll focus on gas cluster ion beams (GCIB).

A GCIB typically consists of thousands of constituent atoms, giving it a collective molecular weight anywhere from 100,000 g/mol upwards. Under typical acceleration voltages (kV), such a large ion moves very slowly, requiring longer pulses and on a conventional ToF would result in poor mass resolution. By running in continuous (or long pulsing) mode, the J105 is able to get around this issue and take full advantage of the benefits of using GCIBs.

The other major advantage of running in DC mode is that focusing the ion beam to a fine spot can be prioritized without affecting the performance of the mass spectrometer. With our most powerful GCIB, the GCIB SM, the optics have been designed to enable spot sizes of just 1.5 µm, combining greater spatial resolution with high-sensitivity mass spectrometry. The benefits of this are clear, and have been highlighted recently by the pioneering work published in Science.

Benefits: Simultaneous high-sensitivity mass spectrometry with high-spatial resolution.

View of a sample through a window

2.      The Extraction Optics

As the primary beam is not pulsed, in order to determine a time-of-flight the secondary ion beam is pulsed instead. This is done by the Buncher, but the extraction optics play a key role is controlling the secondary ion beam prior to that step.

Secondary ions extracted from the surface contain a lot of energy making them difficult to control. In order to form the secondary ions into a controlled beam, they enter an RF quadrupole filled with N2, which slows the ions down through the process of collisional cooling.

This is a crucial step, as it decouples the effects of the primary beam and the sample from the secondary ions. By effectively wiping the memory of any interaction on the surface, this step enables the J105 to analyse samples with complex topography without any loss of mass spec performance.

Benefits: Consistent performance that is independent of ion beam or sample topography.

The analysis chamber of the J105 SIMS

3.      The Buncher

In many ways the heart of the instrument, the Buncher is what takes a continuous stream of secondary ions coming from the quad and forms them into a very short pulse. In order to measure the time-of-flight without pulsing the primary beam or the extraction, the Buncher creates an asymmetric pulse that focuses all ions of the same mass to a single time focus, T0. This is an essential step, and is what ultimately determines the mass resolution.

Benefits: High mass accuracy, high mass resolution.

J105 SIMS reflectron & mass analyser

4.      Tandem MS & Time-of-Flight

As with any form of mass spectrometry, definitively assigning peaks requires a secondary validation step. One way to do this is through tandem MS, whereby a parent ion is selected to undergo fragmentation and the resulting spectrum is used to determine the exact form of the parent. The J105 SIMS was the first SIMS instrument to introduce tandem MS, and is included as standard on all our instruments.

When a user selects an ion of interest, it is directed into a high-energy collision cell filled with N2, producing characteristic fragment ions. Whether running an MS1 or MS2 experiment, ions then enter the 1500 mm long reflectron before being detected.

Benefits: Tandem MS for accurate peak identification, high mass resolution.

The J105 SIMS contains several innovative design features that combine to produce an instrument like no other, optimized to enable both maximum sensitivity and maximum spatial resolution simultaneously from any ion beam. Consistent performance is guaranteed, as the mass spectrometer delivers high mass resolution (> 10,000) and mass accuracy (< 5 ppm) that are completely independent of the ion beam and the sample environment.

The J105 SIMS is the ideal tool for a wide range of applications and sample types, including biological research, pharmaceuticals, thin films, polymers, energy applications and many more. To find out if the J105 might be the right instrument for you, or to arrange a demonstration, please get in touch via our Contact Page.

Cocaine metabolite imaging in fingerprints with Water Cluster SIMS

Detection of drug compounds and their metabolites in natural environments is a critical topic for both forensic and pharmaceutical applications, and requires overcoming some of the limitations in existing microscopic and analytical techniques.

Time of Flight Secondary Ion Mass Spectrometry (ToF SIMS) is a powerful analytical technique capable of providing detailed chemical and spatial information about a surface, and as such has recently been employed in a number of forensic studies for drug and metabolite detection. However, ToF SIMS can suffer from low sensitivity due to insufficient ionisation efficiency, and this is particularly true for complex biomaterials, i.e. those of most interest to forensic and medical analysts.

Recently, we have led the development of a powerful unique gas cluster ion beam (GCIB) using water clusters. The Water Cluster Source is capable of enhancing ion yields by many orders of magnitude compared to other conventional ion beams (C60+, Bi3+ etc.), and is particularly effective for biomolecular imaging and 3D analysis of organics such as tissue, cells, fingerprints, etc.

Plot displaying increase in signal intensity using water clusters
Water clusters enhance sensitivity to intact biomolecules such as lipids, even compared to current state-of-the-art GCIB technology.

In this application note, an experimental fingerprint detection approach using the Water Cluster Source identifies traces of ingested cocaine on human skin. The use of the J105 SIMS equipped with the Water Cluster Source (Water Cluster SIMS) provides both visualisation of the latent fingerprint as well as discrimination between contact-only and ingested cocaine by looking for metabolites of the drug excreted through the skin.

Detectable levels of metabolite in a fingerprint are extremely low, for instance 25 mg of ingested cocaine excretes less than 2.5 ng/mL in sweat,1 and previous attempts using other mass spectrometry imaging (MSI) techniques such as MALDI and DESI were unsuccessful. Using Water Cluster SIMS, it was possible not only to detect the metabolite, but also to generate a high-contrast chemical map of the entire fingerprint.

The fingerprint specimen, provided by University of Surrey, was collected on a piece of silicon wafer from a donor who had previously ingested cocaine,2 then a ToF-SIMS analysis was acquired on an 18×6 mm2 area with a 70 kV (H2O)29k+ primary ion beam in the J105 SIMS.

Figure 1(a) shows the chemical image of the 290.14 m/z signal, demonstrating the characteristic fingerprint features with ridges, valleys, as well as sweat pores. Due to the high mass accuracy of the J105 SIMS, this signal is confidently annotated as the cocaine metabolite benzoylecgonine (BZE, C16H20NO4+). Figure 1(b) shows a colour overlay of BZE (magenta) and the cocaine molecular ion (C17H22NO4+, 304.15 m/z – yellow). As expected, cocaine was observed in particulate form (see arrow) due to direct contact of the donor with the powder, and is not co-localised with BZE.

ToF SIMS image of cocaine metabolite BZE in a fingerprint.
Figure 1(a) Positive ion image of BZE (C16H20NO4+, 290.14 m/z) in a fingerprint. (b) Overlay positive ion image with BZE (magenta) and cocaine (C17H22NO4+, 304.15 m/z – yellow). (c) BZE peak, with high mass accuracy and high mass resolution.

These images, with the small amounts of BZE and cocaine present, demonstrate the benefits of Water Cluster SIMS for enhancing sensitivity, particularly for trace detection of organic compounds in complex sample matrixes.

The J105 SIMS is a powerful tool for 2D and 3D molecular imaging, providing high sensitivity analysis with a range of powerful features. Now featuring the new Water Cluster Source, the J105 takes another leap forward to offer even greater sensitivity and to intact molecular ions. This exciting new technology has been shown to dramatically improve the imaging of drug metabolites ingested by the body, and is a powerful tool for visualising molecular information in a wide range of applications.

To find out more about how the J105 SIMS can benefit your research, get in touch via our Contact Page.


  1. Kacinko, S. L., Barnes, A.J. et al. , Disposition of Cocaine and Its Metabolites in Human Sweat after Controlled Cocaine Administration, Clinical Chemistry, 51, 2085 (2005).
  2. Jang, M., Costa, C., Bunch, J. et al. On the relevance of cocaine detection in a fingerprint. Sci Rep 10, 1974 (2020).

High-resolution multi-omics profiling of individual cells

In a landmark publication, Tian et al. demonstrate the feasibility of combined GCIB/C60 SIMS imaging for multi-omics profiling in the same tissue section at the single-cell level.

A new approach

Multi-omics data are vital to understanding normal regulatory processes and are essential for designing new anti-cancer modalities. Unfortunately, sample preparation methods between different omics are typically incompatible. As such, it is nearly impossible to correlate multiple omics profiles within the same sample, let alone their spatial co-localisation at the single-cell level.

The new approach developed by Tian et al. thus represents a significant leap forward.

The study, reported in the journal Analytical Chemistry, uses a multimodal approach using the J105 SIMS to correlate different cell types. First, water cluster SIMS maps the lipids and metabolites in individual cells. Then, multiplexed SIMS imaging with a high-resolution C60 beam maps the same tissue section stained by lanthanide tagged antibodies.

Close up picture of a microscope

Multiplexed SIMS imaging involves linking specific lanthanide isotopes to antibodies and applying them to the tissue. Subsequent SIMS imaging of the lanthanides maps multiple cellular epitopes at sub-cellular resolution.

The combined approach of water cluster SIMS plus multiplexed ion beam imaging on the same tissue section enables mapping lipids, proteins, and metabolites at the single-cell level.

High-resolution multi-omics

Cryogenic water cluster SIMS was conducted on the J105 SIMS at 1.6-micron beam spot size on fresh frozen sections of invasive ductal carcinoma/ductal carcinoma in situ (IDC/DCIS) tissue. This analysis was followed by staining with lanthanide-tagged antibodies on the same frozen-hydrated tissue and imaging the same region using a C60 beam with a 1.1 µm spot size.

Workflow schematic. The frozen-hydrated IDC/DCIS sample is first analysed using water cluster SIMS with a 1.6 µm spot size. The sample is then stained with lanthanide-tagged antibodies and imaged with C60-SIMS with a 1.1 µm spot size. Image reproduced from Anal. Chem. 2021, 93, 23, 8143-8151.

The first results

Water cluster SIMS revealed the distributions and intensities of more than 150 lipids and important metabolites up to m/z 2000. HCA analysis revealed considerable variation between the location of cluster SIMS identified ions and the nine C60-SIMS cell markers.

This work represents the first successful attempt to profile proteins, lipids, and metabolites on the same tissue at the single-cell level. GCIB-SIMS, especially water clusters, has demonstrated its unique ability to detect lipids and metabolites in biological samples at unprecedented resolutions.

Picture of a person placing a sample into the J105 SIMS

Using a combined SIMS imaging approach enables the correlation of different cell types with their metabolic and lipidomic status. It offers valuable information about proteins, lipids, and metabolites on the same sample and at the same resolution.

The J105 SIMS provides a unique platform for this multimodal SIMS approach. The only instrument to offer water cluster SIMS plus multiplexed ion beam imaging, the J105 also provides high mass accuracy and tandem MS capabilities for accurate ion assignment.

Read the complete publication here.

Experience the capabilities of the J105 SIMS for yourself by booking a demonstration. Get in touch with our sales team today to organise your demo.

Analyse v2.0.2.15 Release

We are happy to announce the release of Analyse v2.0.2.15 for all J105 SIMS customers. This long awaited release brings with it a host of new features as well as several bug fixes. Chief among the new features is a new imzML file converter. To download the new release, simply go to our downloads page and click on the link.

Why you shouldn’t overlook C60 beams just yet

C60 cluster ion beams are a fantastic tool for analyzing both hard and soft materials. Composed of sixty carbon atoms arranged into a football shape, C60 ions combine several different features making it a great all-rounder ion beam. This is why we always recommend customers to consider including a C60 beam when specifying their J105.

As the C60 molecule is larger (approx. 7 Å) than the lattice constant for most materials, it does not experience channeling the way smaller ions such as bismuth do. As such C60 beams exhibit incredibly uniform sputter rates across a wide range of materials, and even on challenging poly-crystalline materials where there is a range of crystal orientations.

As a cluster ion, C60 also produces very shallow craters with very little, if any, subsurface damage, so etch cycles are not needed to remove damaged layers when performing depth profiles or 3D imaging. As the J105 samples 100% of the analysis volume, high sensitivity is guaranteed, and combined with spot sizes as low as 300 nm, C60 is a powerful beam for delivering maximum resolution in 2D and 3D.

NiCr Standard Depth Profile C60
C60 depth profile through the NIST NiCr standard showing <5 nm depth resolution. As there is no need to perform etch cycles to remove damaged layers, depth resolution on the J105 is limited only by the crater depth of the ion beam.

The figure below shows a 3D image of a semiconductor stack alongside a depth profile through the same, performed with a 40kV C60 beam in positive ion mode. The sample consists of layers of InSb, Al, and GaAs respectively, covered in a protective photoresist layer.

3D SIMS image of InSbAlGaAs Stack with depth profil
The J105 has one mode of operation, so amazing 3D images, high-resolution 2D images, as well as detailed depth profiles can all be obtained from a single data set.

The resulting 3D SIMS image shows the layers in amazing clarity, with very sharp interfaces. As the J105 always samples 100% of the analysis volume, high sensitivity is guaranteed. The detailed depth profile through the sample also shows the presence of dissolved Al within the InSb layer, as well as the presence of Sb in the pure Al layer.

The 40kV C60 beam is ideal for this type of sample or application due to the combination of soft organic, inorganic, and hard metallic layers within the same sample. Combined with spot sizes as low as 300 nm, C60 is a powerful beam for delivering maximum resolution in 2D and 3D, no matter what type of sample you have.

Drug detection with high-sensitivity using ToF SIMS

The high attrition rate of pharmaceutical drug compounds adds enormously to the cost of those that make it to market, so there is an urgent and growing need to identify failure at earlier stages of drug development.

In order to do so, researchers require as much information as possible. Specifically, there is a need to measure the concentration of a drug at the target in order to accurately predict its pharmacological effect. This then requires a means of generating label-free sub-cellular imaging, as fluorescent labels may affect drug chemistry, altering results.

Time of flight secondary ion mass spectrometry (ToF SIMS) is a powerful tool for label-free chemical imaging, having typically very high lateral resolution capable of resolving sub-cellular features with 3D analysis capabilities.

ToF SIMS is thus a potentially powerful analysis tool for the screening of new drug compounds. However, the use of high energy projectiles for ToF SIMS analysis can cause molecules to fragment, preventing the molecular ion from being detected. This can lead to a lot of ambiguity, for example distinguishing between a drug compound and its metabolites.

Another possible stumbling block is the issue of sensitivity, particularly for those compounds of most interest. In a recent study by the National Physical Laboratory (NPL), Vorng et al. demonstrate that the sensitivity in ToF SIMS is proportional to the Log P of that compound, such that compounds with low or negative Log P values are extremely difficult to detect.  

Log P, or partition coefficient, is a measure of hydrophobicity, and is a major factor used in pre-clinical assessment of a compound’s druglikeness.  It is advisable that a drug candidate be as hydrophilic as possible while still retaining adequate binding affinity to the therapeutic protein target, i.e. that the Log P be as low (or negative) as practicable. This presents an obvious problem for the use of ToF SIMS as an analytical tool in this context.

Cluster beam colliding with a surface.

We have recently led the development of a new type of ion source for ToF SIMS that provides unparalleled sensitivity particularly for organic species. Available exclusively on the J105 SIMS, the Water Cluster Source simultaneously reduces fragmentation while increasing ionization, for truly unparalleled sensitivity of drugs, metabolites, biomarkers, lipids, peptides and more.

Combining this new ion source with the already impressive sensitivity of the J105 SIMS, even low Log P compounds can be detected in tissue and cells, with direct, label-free imaging of the molecular compounds at sub-cellular resolutions.

To demonstrate this, we doped tissue homogenate with 4 different pharmaceutical compounds that span the range of Log P from -0.8 to 7.6. The relationship between sensitivity and Log P reported by NPL is observed in this data, however the slope of the line is greatly reduced, with only a factor of 40 between the highest and lowest values.

ToF SIMS sensitivity to drugs as a function of Log P
ToF SIMS sensitivity of four different drugs using the Water Source. Sensitivity shows a linear relationship to the partition coefficient, Log P, though the slope is not steep.

As a comparison, we performed the same experiments with a state-of-the-art Ar gas cluster ion beam and plotted the yield against that of the new Water Source. The Water Source increased sensitivity by an order of magnitude in most cases, with the largest increase being for those compounds with the lowest Log P values. This indicates that the improvement in sensitivity is greatest for those compounds that need it the most.

Comparing sensitivity of argon and water cluster beams for four different drugs
Comparing sensitivity of a state-of-the-art Ar cluster source with the Water Source. Sensitivity improves by roughly an order of magnitude when using water, with the largest increase for those compounds with lower Log P values.

As a final demonstration of the capabilities of the J105 with the Water Source, we performed tandem MS analysis on the homogenate samples. Tandem MS is an important step for confirming any assignment in mass spectrometry, however the inefficiency of the process often means it can only be performed on high intensity peaks. With the boost in sensitivity provided by the Water Source, tandem MS analysis is possible even on compounds with relatively low Log P values, such as ciprofloxacin.

Tandem MS analysis of the drug ciprofloxacin
Tandem MS performed on the J105 SIMS with a Water Source. Greater sensitivity allows definitive confirmation of many more peaks.

ToF SIMS is a potentially powerful analysis tool for the screening of new drug compounds, however research is hampered by the inherently low sensitivity to many drug candidates. The J105 SIMS in combination with the Water Cluster Source provides unparalleled sensitivity to drug compounds, particularly in complex matrices such as tissue and cells, even for low Log P compounds. This unprecedented sensitivity combined with sub-cellular imaging and high-resolution 3D imaging mean the J105 SIMS is a powerful tool for drug analysis.

To learn more about how the J105 SIMS can benefit your research or to set up a demonstration, get in touch via our Contact Page.

High-resolution molecular imaging ToF SIMS

Historically ToF SIMS has not been sensitive to intact molecules due to the excessive fragmentation caused by the primary ion beam. Now however, thanks to the progress in gas cluster ion beam (GCIB) technology over the last decade, sensitivity to intact molecular species in ToF SIMS has increased by several orders of magnitude, making it possible to achieve molecular imaging with the high-spatial resolution traditionally associated with SIMS.

The development of high-energy gas cluster beams with small spot sizes has dramatically altered the sensitivity to intact molecular species. This is enabled by the unique design of the J105 SIMS, which allows any ion beam to be used without impacting performance. So large gas cluster beams may be used while still maintaining high mass resolution, and thereby greatly improving molecular sensitivity.

It is now possible to map the distribution of lipids in biological tissue with higher resolution than ever before. This is illustrated in Figure 1, where two sphingolipid species and a glycerophospholipid species are imaged within rodent cerebellum tissue. The inset line scan demonstrates the sharp drop off in C24-OH signal, on the order of a few microns, giving researchers unparalleled clarity into the structure of their sample.

Figure 1. 2 μm per pixel lipid mapping in rodent brain tissue, analysed using a 40kV Ar4000 beam. Boundaries between sphingolipid species C24 (m/z 890.6 – blue), and C24-OH (m/z 906.6 – green), and the glycerophospholipid species PI(38:4) (m/z 885.6 – red) are clearly resolved. Inset: line scan drawn across the C24-OH signal. Data courtesy of the University of Gothenburg.

As damage to the sample molecules is minimised, a volume of material can be analysed, not just a static dose limit, resulting in higher signals and the ability to depth profile without wasting material. Significantly, for a given dose, larger cluster beams have been shown to produce higher signals from most large molecules, as illustrated in Figure 2.

Figure 2. High signal intensity with low fragmentation. (a) Normalised signal intensity for molecular and significant fragment signals from Irganox 1010 with an Ar4000 beam, showing much higher ion yields for higher beam energy. (b) Normalised signal ratios comparing levels of fragmentation for four different beam energies. Data courtesy of the University of Gothenburg.

Figure 3 shows the mass spectrum and corresponding image of the DG region of a rodent hippocampus. Using a 30 kV [CO2]3k+ beam, the distribution of GM1(36:1), GM1(38:1), and ST(18:0) were mapped at a pixel density of 2 μm per pixel. A wealth of information is contained within the spectrum, with detailed phospholipids, cardiolipin species, and high-mass ganglioside species all clearly present and identified.

Figure 3. Negative SIMS spectrum and corresponding image from DG region of rodent hippocampus, showing the range of phospholipid, ganglioside, and cardiolipin species detected. Analysis performed using a 30 kV [CO2]3k+ beam at 2 μm per pixel. Data courtesy of Pennsylvania State University.

Large molecular species such as lipids play an important role in basic cellular processes. As such it is crucial to have the correct tools with which to study these systems. The J105 SIMS, alongside the development of new gas cluster ion sources, is pushing the capabilities of ToF-SIMS, both in terms of the mass detection limits, and the limits of spatial resolving power, enabling researchers to probe further and discover more.

For further information about our instruments or to arrange a demonstration, please get in touch via our Contact page.

Detecting pollutants in a Cherry Blossom leaf

Plant samples such as leaves are a challenging sample for ToF SIMS. Composed of insulating materials such as cellulose (cell walls) and lipophilic coatings (cuticular layer), charge build up can affect measurement quality. Using an electron gun during analysis can alleviate the charging effect and enables 3D analysis of the surface of a leaf.

Cherry blossom leaves (Prunus serrulata) collected in a busy city were analysed on the J105 SIMS using a 40 kV C60 ion beam. Pieces of blossom leaves were mounted onto double sided tape, attached to a sample stub, and gently pressed down in the corners to ensure best possible contact without deforming the leaf surface. Overview images were acquired on both sides of the leaf surface, with a spatial resolution of 1 µm per pixel and a primary ion dose of 2.2×1013 ions/cm2.

Experimental Conditions

Ion Beam:40kV C60+
Dose:2.2×1013 ions/cm2
Spatial Resolution:1 μm
Charge Compensation:60V Electron Gun, 25V Stage Bias

Without charge compensation, no secondary ions could be detected. Applying an ever-increasing stage bias would produce secondary ions temporarily. Only a combination of charge compensation methods via a 25 V pulsed stage bias and electrons emitted at 60 V beam energy enable us to generate an image of the leaf surface as well as steady signal during depth profiling.

Figure 1. Analysing the surface of a cherry blossom leaf.

Surface analysis reveals the outline of single plant cells. The outlines of the cells contain CaOH (m/z 56.97), while inorganic compounds such as K2O+ (m/z 93.92), Na2Cl+ (m/z 80.95), and Fe+ (m/z 55.93) are unevenly dispersed on the surface of the leaf. All compounds identified across the uneven leaf surface have a mass accuracy < 5 ppm (Table 1).

Analysis also revealed the surface to be coated with an even layer of organic compounds represented by molecules containing aromatic structures, e.g. tropylium ion, C7H7+ (m/z 91.05). Wax coatings on plants take the form of long aliphatic carbon chains, so aromatic structures such as these are unexpected and may indicate the presence of gasoline pollutants such as BTX (benzene, toluene, xylene).

Analysis of complex, insulating, and uneven samples such as these is made routine on the J105 SIMS.

Depth profile analysis reveals that as the cells are etched away, the layer of aromatic compounds reappears on the underside of the sample. Additionally, potassium containing substances are detected that are not present on the surface and only occur within certain cell walls (Figure 1 inset, green).

Imaging depth profile through a leaf showing CaOH (red), K2O (green), and C7H7 (blue).

Repeating the analysis on the lower epidermis reveals a high concentration of aromatic signals surrounding the stomata (Figure 2, green). It is known that plants can absorb pollutants such as BTX, mainly through the stomata, giving further evidence to the origin of these compounds.

Analysis of lower epidermis. Concentration of aromatic signals such as C7H7+ around the stomata may indicate uptake of pollutants such as BTX.

Analysis of complex, insulating, and uneven samples such as these is made routine on the J105 SIMS. Performing high-resolution 3D analysis with high sensitivity creates a more complete picture, enabling a greater understanding of the sample and its environment.

We gratefully acknowledge NESAC/BIO and the University of Washington for the use of their data in this work.

For further information about our instruments or to arrange a demonstration, please get in touch via our Contact page.

ToF SIMS of Rough or Uneven Samples

A common problem faced by TOF SIMS analysis is loss of peak resolution and mass accuracy on samples with rough or uneven topography. The J105 SIMS does not suffer from these issues, experiencing no loss in mass accuracy across even the roughest of samples

The ability to obtain consistent, accurate results is key to all analytical techniques, and none more so than ToF SIMS. Providing detailed chemical information about a surface, ToF SIMS is an extremely versatile surface analysis technique. The results, however, can be very sensitive to sample environment; insulating samples, or changes in sample height can affect the measurement and result in inconsistent, or inaccurate results.

In this application note we explain the reasons why sample roughness can be a problem, and show how the unique design of the J105 SIMS has solved this issue.

Why Roughness is a Problem for ToF SIMS

Time of flight mass spectrometers determine the mass-to-charge ratio of ions by measuring the time taken to travel a known distance under an electric field. The accuracy of this measurement – known as the mass-resolution – is determined by how precisely this flight time can be measured.

In conventional ToF SIMS, good measurement accuracy is achieved by generating very short pulses (in nanoseconds) of the primary ion beam. If the sample is completely uniform, the variation in flight time of ions with the same mass will be minimal. Thus the experiment will be quite accurate.

Say that our sample is not uniform however, but has a height variation caused by a slight tilt when mounting. In this case, ions of equal mass coming from different parts of the sample will have to travel slightly different paths, and thus will have slightly different flight times. Our experiment will not be as accurate this time, and will show broader peaks as ions of the same mass arrive at slightly different times.

What about a sample with a lot of surface roughness or height variation, such as the surface of a meteorite, or a coronary stent? In these cases it should be clear that accurate results will be difficult to obtain.

There is also a secondary issue caused by samples with rich topography, particularly those that are naturally insulating. Topographic features may result in the build up of localized surface charge. This localized charge distorts the local electric field, and can thus affect the flight path of ions at these locations.

Solving the Problem: Decoupling The Mass Spectrometer

Animated GIF of J105 SIMS Operation

Schematic of the J105 SIMS operation, illustrating the path of primary (green) and secondary (red and blue) ions through the instrument.

In order to solve this problem, the sample and its environment must be decoupled from the mass spectrometer. However, in order to do this, a new method of producing the first time-focus is required.

The J105 SIMS has been designed such that the primary beam is decoupled from the time-of-flight measurement. Instead, a shaped-field buncher and timed ion gate sit after the electrostatic analyzer, generating the first time-focus for the time-of-flight measurement. By cooling the ions prior to passing them into the buncher, the energy spread is reduced to within 1 eV, removing any effects of the sample.

As a result of this design, the distance traveled by the ions prior to reaching the spectrometer has no effect on the measured flight time. The mass spectrometer is therefore independent of the local environment on the sample.  This thus enables the J105 to analyze otherwise challenging samples, producing consistent, accurate results with no loss of resolution.

The following examples demonstrate the capabilities of the J105 to analyse rough, uneven, topographic samples without compromising mass resolution or mass accuracy.

Example #1: M1.6 Screw Thread

The figure below shows the total ion image as obtained from an M1.6 screw thread. This sample was chosen for its difficult topography, having a thread depth of approximately 300 μm. Despite the challenging nature of the sample, highly consistent results are obtained no matter what point on the surface is chosen.

The spectrum surrounding the Cr+ peak (nominally 51.94051 amu) is shown to the right of the image for a range of selected areas across the sample. The areas chosen span the full 300 μm depth of the screw thread.

Despite this large variation in height across the sample, the variation in peak center across the chosen points is only 0.0002 amu, which corresponds to a mass error of less than 5 ppm across the complete depth range.

Total Ion Image of M1.6 screw thread

Left Total ion image of an M1.6 screw thread, obtained on the J105 SIMS. Right Comparison of the Cr+ peak (nominal mass 51.94051 amu) from spectra obtained at various locations across the screw thread sample (height variation approximately 300 μm). Variation in mass accuracy across the 300 μm depth range of the sample shows less than 5 ppm deviation from the nominal value.

Example #2: Frog Embryo

The figure below shows the total ion image of a frog embryo during multiple stages of development over a 5.5 hr period. The embryo is a sphere approximately 1.1 mm in diameter – a very challenging samples for ToF SIMS.

Despite the challenging nature of the sample, uniform signal is obtained from almost all areas of the hemisphere without affecting the mass calibration.

Total ion image of developing Xenopus laevis embryo

Total ion image of a Xenopus laevis embryo at various stages of development, from 2 cells to many. Embryo is approximately 1.1 mm in diameter, in a field of view of 1200 x 1200 μm. Strong signal is obtained from all parts of the hemisphere, and the mass calibration did not change over the image. This research was originally published in the Journal of Lipid Research. Tian, H. J. Lipid Res. 2014. 55: 1970-1980. Published with permission from original author.


Rough, uneven, or highly topographic samples can cause problems in ToF SIMS analysis, resulting in loss of mass accuracy and mass resolution. Unfortunately, most real world samples tend not to be perfectly uniform.

The J105 SIMS solves this problem by decoupling the mass spectrometer from the primary beam, thereby removing any effects of the sample from the time of flight measurement. The result is a ToF SIMS capable of analyzing rough, topographic samples without compromising mass resolution or mass accuracy.

The J105 SIMS combines flexibility with high performance, delivering unprecedented performance on biological and inorganic samples alike. For more information, visit the J105 product page, read our Application Notes, or Contact Us to discuss your interest further.

Depth Profiling in ToF-SIMS with the J105 SIMS

Depth profiling is a powerful technique in surface analysis for examining interfaces and exploring the 3-dimensional structures of a material, to which SIMS is uniquely suited.

Many modern instruments are equipped with a sputter ion beam in addition to their primary analysis beam for depth profiling. This enables users to perform “etch-cycles” in-between analysis cycles, thereby building up a stack of 2D images and generating a 3-dimensional view of the sample.

There are limitations to the use of SIMS for depth-profiling however. Unlike non-destructive techniques such as XPS, SIMS alters the surface during analysis. In fact, fragmentation and migration of species can occur up to 20 nm below the surface. Etch-cycles therefore perform several duties. 1. They enable 3D image capture in a realistic time-frame, and 2. they remove the damaged layers, leaving behind a relatively clean surface for the subsequent analysis cycle. This process has some obvious drawbacks, most notably that a significant amount of material is lost during each cycle. This can severely limit the depth resolution.

As the J105 SIMS uses a dual-stage ToF analyzer, any beam may be employed as the primary analysis beam, including C60 and gas cluster beams. In this case, additional etch-cycles are not required – analysis and low-damage etching are continuous and concurrent. This means that no data is lost and all the material is sampled, making the J105 SIMS an extremely accurate tool for depth profile analysis.

No etch-only cycles on the J105 SIMS

As the J105 uses a DC beam, there is no need to interlace an etching beam with the analysis beam as analysis and low-damage etching are continuous and concurrent.

Organic Samples

In 2015, NPL led a VAMAS study comparing compositional analysis of an organic layered structure using both SIMS and XPS. The stack consisted of layers of Irganox 1010 and either Irganox 1098 (denoted MMK) or Fmoc-pentafluoro-Lphenylalanine (denoted MMF) in well defined ratios.

Chemical structure of Irganox 1010 and Irganox 1098

Chemical structure of (a) Irganox 1010, and (b) Irganox 1098.

Compared with a number of instruments using a Bin+ analysis beam, the J105 SIMS, using a 40 kV Ar4000+ beam, achieved the highest depth resolution of any instrument, demonstrating 12.8 nm. The figure below shows an example depth profile of such an organic stack structure.

VAMAS depth profile using J105 SIMS

Depth profile of a stacked Irganox 1010/Irganox 1098 sample. The J105 SIMS demonstrated a depth resolution of 12.8 nm – the highest of any instrument in the study.

HeLa cells

Depth profiling may also be used to produce 3D chemical maps of complex structures. The example below shows a 3D reconstruction of HeLa cells – an immortal human cervical cell line. The lipid phosphocholine head group (m/z 184.1), shown in green, represents the cell membrane, while the nucleic acid adenine (m/z 135.1), shown in red, represents the nucleus.

3D chemical map of HeLa cells

3D chemical mapping of HeLa cells using a 40 kV C60 beam. Phosphocholine (m/z 184.1 – green) and adenine (m/z 135.1 – red) represent membrane and nucleus respectively. Data courtesy of John Fletcher.

Such 3D reconstructions, detailed by Fletcher, Rabbani, and Henderson et al. here, require extensive post-processing of the data to convert the 2D layers – which have no height information – into a 3D image that is representative of the actual structure. The result, however, is a stunning reconstruction of the cell structure, that is made possible by the ability of the J105 SIMS to capture a complete spectrum from each voxel without loss of data.

The animation below reveals how the cell membrane is gradually removed to reveal the internal contents – in this case, depicted by the void created in cells.

Animated GIF of depth profile through HeLa cells with J105 SIMS

Depth profiling through HeLa cells using a 50 kV (CO2)5000+ beam at 1 μm per pixel. The lipid layer (phosphocholine) @ m/z 184.1 – representing the cell membrane, is gradually etched away, revealing the contents of the nucleus (adenine) @ m/z 135.1. Data courtesy of Hua Tian.

Inorganic Samples

The properties of poly-atomic ion beams such as gas clusters and C60+ are particularly useful for the analysis of organic samples, and have allowed molecular depth profiling to become a reality. However, that does not mean that such ion beams do not also provide benefits on inorganic samples. In fact, C60 ion beams are uniquely useful for use on both organic and inorganic samples.

Sputtering under C60+ has been shown to be less sensitive to variation in material, incidence angle, and crystallinity of the sample and has been show to offer improvements in quantitation and reproducibility on glass/mineral standards, and therefore provide an excellent solution for depth profiling on these types of samples.

NIST Ni:Cr Standard

The performance of 40 keV C60+ on a metal multilayer sample is demonstrated on the Ni:Cr standard reference material from NIST. The sample comprises alternating layers of Ni and Cr on a silicon wafer substrate. The plot on the left shows the signal from the m/z 52, and 58 mass channels corresponding to the Cr and Ni respectively. The Ni layers are 66 nm thick and the Cr layers 53 nm. A depth resolution of ca. 5 nm is calculated (16-84% rising edge of 1st Ni layer). This is close to the expected crater depth of a single C60+ impact.

Depth profile through NIST Ni:Cr standard with J105 SIMS

40 keV C60+ depth profile through the NIST Ni:Cr standard showing < 5 nm depth resolution.

Mixed Metal Oxide Sample

The example below is a depth profile through a mixed metal oxide material of relevance in hydrogen fuel cell fabrication. The experiment was performed using a C60+ 40 keV primary ion beam rastered over a 150 × 150 µm2 field of view. The J105 provides excellent signal to noise as all the material is collected during the depth profile similar to a dynamic-SIMS instrument but with the parallel mass detection and mass range of a time-of-flight analyzer. Decoupling the mass spectrometry from the ion generation process also means that the mass resolution is not compromised, and mass accuracy and calibration does not drift as the sample is eroded. Depth profiles and 3D images are generated retrospectively from the “image stack” with the outermost pixels discarded to remove any crater-wall artifacts.

Depth profile through fuel cell using J105 SIMS

Variation in secondary ion signal as a function of primary ion beam fluence for Cr+, Fe+, CeO+, and TiO+ displayed in the profile and 3D reconstruction in green, grey, red, and blue respectively. 150 x 150 μm2 field of view, z depth approximately 600 nm.

The composition of this sample is in fact much more complex than shown in the above plot and 3D rendering, and contains Al, Mn, Cr, Ce, Fe, Ti and oxides of these metals all of which are observed clearly in the mass spectra through the profile, in addition there is a thin layer of Na and K on the very surface of the sample (not shown).


The J105 SIMS provides an excellent solution for depth profiling of samples. The ability to use a variety of cluster beams for continuous and concurrent analysis and low-damage etching, without the need for “etch-only” cycles, enables high depth resolution on any sample type. If you would like more information, or would like to speak to a member of our team, please get in touch via our Contact page.

ToF-SIMS Analysis on Insulating Samples

Performing ToF-SIMS analysis on insulating samples can be particularly challenging. Surface charge can impact the accuracy of the results, or in the worst cases prevent any results being obtained. Thanks to its unique ToF design, the J105 SIMS is capable of imaging highly insulating samples without loss of signal or performance.

The Problem

Insulating samples provide a particular challenge for the ToF-SIMS user. A charged beam of particles impinging a surface necessarily produce a surface charge, both by emission of secondary electrons and by transfer of charge to that surface. For a metallic sample this charge is easily dissipated into the surrounding bulk, however this is not the case for insulating materials where there are no free electrons to neutralize the charge. The result is a build up of surface charge that can have a number of deleterious effects on a ToF-SIMS experiment.

For instruments where the time reference is determined by the primary beam pulse, regions of surface charge can affect the flight time of ions ejected from the surface, thereby negatively impacting on the mass-accuracy of the experiment. This effect is particularly pronounced around regions of topography where field strength is enhanced – in the worst case this leads to highly distorted fields preventing ions from ever reaching the detector. The most prominent effect of surface charge, however, is the suppression of secondary ion signals due to field suppression and/or neutralization prior to extraction.

The Solution

Thanks to its unique ToF design, the J105 SIMS is capable of imaging highly insulating samples without loss of signal or performance.

ToF Design

As the J105 does not rely on a pulsed primary beam as a time reference, temporal aberration in the extraction gap, caused by sample charging or other effects, has no impact on the mass accuracy. This enables a large extraction gap and a low extraction field, which in turn mean the extraction optics can accept ions leaving the sample up to very large angles from the normal, increasing transmission. The overall result is consistent performance across the entire sample, even those areas with lots of topography.

Insulating Sample Fig

Schematic illustration of the various means by which the J105 SIMS can compensate or accommodate charging samples.

Charge Compensation

Charge compensation/neutralization may be used to alter the effects of surface charge and improve signal on charging samples; this can be achieved by sample biasing and/or low-energy electron bombardment. In sample biasing, the sample stage is biased up to ± 100 V to compensate for the field created by the surface charge. This requires that the bias voltage is able to reach the sample surface, and so may not be effective on thicker samples or in situations where conductive tracks are prohibited.

Alternatively, pulses of low-energy electrons may be interlaced between the primary beam, in a pseudo-DC mode, to directly neutralize the charge on the surface. This has advantages in that the electrons are naturally drawn to localized pockets of charge, providing a “self-limiting neutralization” mechanism. One must be careful however, as even low-energy electron beams may result in damage to fragile organic structures. Generally speaking, in most situations, it is best to use a combination of both techniques, experimenting to find the correct balance for each individual sample.

Insulating Samples

Sodium Citrate Crystal

The figure below shows SIMS images of a single sodium citrate crystal on a substrate of double-sided tape – both highly insulating materials. Using a combination of sample bias and electron flood gun to neutralize surface charge, good signal levels are obtained from all areas without loss of mass accuracy or mass resolution, despite the highly topographic surface, enabling the identification of small micro crystals of NaCl within the sample.

Sodium Citrate SIMS image

SIMS images of a single sodium citrate crystal on double-sided tape, obtained with a 40 kV C60+ beam, showing (left) total secondary ion image, (middle) Na2OH (m/z 62.985), and (right) Na2Cl (m/z 80.95 + 82.95).

Polished Rock Surface

The second example shows a SIMS overlay image of a polished rock surface. The image is a 1 x 1 mm area, taken at 1024 x 1024 pixels using a 40 kV C60+ beam. A combination of electron flood gun, and sample bias was used in this instance, with +60 V applied to the stage in order to compensate for the effects of charging. A number of elements and minerals are identified in the image, including K, Ca, SiOH, Mn, Fe, and TiO.

SIMS image of rock surface

SIMS overlay image of a polished rock surface, imaged with a 40 kV C60+ beam. A combination of a low-energy electron flood gun and sample biasing was used to optimise imaging conditions for this insulating sample. Elements and minerals visible include: K (green), Ca (yellow), SiOH (red), Mn (cyan), Fe (white), and TiO (blue). Data courtesy of Dan Graham & Tina Angerer.

Mass Accuracy

Despite the charging nature of this sample, consistent mass accuracy is maintained across the data set. This is illustrated in the figure below, where three peaks, TiO, Na2O, and C5H2 respectively, are identified with sub 5 ppm accuracy. As evidenced by the overlay image accompanying the spectrum, all three peaks are spatially distributed throughout the sample. Spatial resolution, mass resolution, and mass accuracy all combine to make peak identification a routine procedure, even on challenging samples such as this.

Mass accuracy on insulating samples

SIMS overlay image & spectrum of polished rock surface. Even on highly insulating samples such as this, high mass accuracy (<5 ppm) is maintained at all points, enabling identification of numerous mineral fragments and organic species. Data courtesy of Dan Graham & Tina Angerer.


Real-world samples – where sample charging and topography are unavoidable – have always posed a challenge to reliable ToF-SIMS analysis. Now, through innovations in instrument design and engineering on the J105 SIMS, analysis of such samples is becoming routine, giving you more time to focus on solving the important problems. If you would like more information, or would like to speak to a member of our team, please get in touch via our Contact page.






IOG C60-40


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