Mass spectrometry imaging is a field that promises to become a mainstream bioanalysis technology by allowing the combination of single-cell imaging and subcellular quantitative analysis. The frontier of single-cell imaging has advanced to the point where it is now possible to compare the chemical contents of individual organelles in terms of raw or normalized ion signal. However, to realize the full potential of this technology, it is necessary to move beyond this concept of relative quantification. Here we present a nanoSIMS imaging method that directly measures the absolute concentration of an organelle-associated, isotopically labeled, pro-drug directly from a mass spectrometry image. This is validated with a recently developed nanoelectrochemistry method for single organelles. We establish a limit of detection based on the number of isotopic labels used and the volume of the organelle of interest, also offering this calculation as a web application. This approach allows subcellular quantification of drugs and metabolites, an overarching and previously unmet goal in cell science and pharmaceutical development.

An important application field of secondary ion mass spectrometry at the nanometer scale (NanoSIMS) is the detection of chemical elements and, in particular, metals at the subcellular level in biological samples. The detection of many trace metals requires an oxygen primary ion source to allow the generation of positive secondary ions with high yield in the NanoSIMS. The duoplasmatron oxygen source is commonly used in this ion microprobe but cannot achieve the same quality of images as the cesium primary ion source used to produce negative secondary ions (C(-), CN(-), S(-), P(-)) due to a larger primary ion beam size. In this paper, a new type of an oxygen ion source using a rf plasma is fitted and characterized on a NanoSIMS50L. The performances of this primary ion source in terms of current density and achievable lateral resolution have been characterized and compared to the conventional duoplasmatron and cesium sources. The new rf plasma oxygen source offered a net improvement in terms of primary beam current density compared to the commonly used duoplasmatron source, which resulted in higher ultimate lateral resolutions down to 37 nm and which provided a 5-45 times higher apparent sensitivity for electropositive elements. Other advantages include a better long-term stability and reduced maintenance. This new rf plasma oxygen primary ion source has been applied to the localization of essential macroelements and trace metals at basal levels in two biological models, cells of Chlamydomonas reinhardtii and Arabidopsis thaliana.

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The green micro-alga Chlamydomonas reinhardtii is commonly used as a model to investigate metallic stress in photosynthetic organisms. The aim of this study was to explore processes implemented by three C. reinhardtii strains to cope with cadmium (Cd), and particularly to evidence Cd sequestration in the cell. For that, we used a combination of subcellular fractionation and chemical imaging (micro X-ray fluorescence (μXRF) and transmission electron microscopy (TEM/X-EDS)) to identify subcellular compartments of Cd accumulation, and X-ray absorption spectroscopy (XAS) to determine chemical Cd speciation. C. reinhardtii wild type strain 11/32b (wt), a newly design strain (pcs1) expressing a modified phytochelatin synthase in the chloroplast and a cell wall less strain CC400 (cw15) were exposed to 70 μM Cd. At this Cd concentration, cell vitality was not affected, however, the strains showed various strategies to cope with Cd stress. In wt, most of Cd was diffused in the whole cell, and complexed by thiol ligands, while the other part was associated with phosphate in vacuolar Ca polyphosphate granules. Thiol ligands increased with exposure time, confirming their important role in Cd stress. In pcs1, Cd was also present as vacuolar Ca polyphosphate granules, and diffused in the cell as Cd-thiol complexes. In addition, while it should be regarded with caution, a minor proportion of Cd complexed by carboxyl groups, was potentially provided by starch produced around the pyrenoid and in the chloroplast. Results suggested that pcs1 uses thiol compounds such as PC to a lesser extent for Cd sequestration than wt. In cw15, an excretion of Cd, Ca polyphosphate granules has to be considered. Finally, Cd was detected in the pyrenoid of all strains.

Mixotrophic microorganisms are able to use organic carbon as well as inorganic carbon sources and thus, play an essential role in the biogeochemical carbon cycle. In aquatic ecosystems, the alteration of carbon dioxide (CO2) fixation by toxic metals such as cadmium – classified as a priority pollutant – could contribute to the unbalance of the carbon cycle. In consequence, the investigation of cadmium impact on carbon assimilation in mixotrophic microorganisms is of high interest. We exposed the mixotrophic microalga Chlamydomonas reinhardtii to cadmium in a growth medium containing both CO2 and labelled 13C‐[1,2] acetate as carbon sources. We showed that the accumulation of cadmium in the pyrenoid, where it was predominantly bound to sulphur ligands, impaired CO2 fixation to the benefit of acetate assimilation. Transmission electron microscopy (TEM)/X‐ray energy dispersive spectroscopy (X‐EDS) and micro X‐ray fluorescence (μXRF)/micro X‐ray absorption near‐edge structure (μXANES) at Cd LIII‐edge indicated the localization and the speciation of cadmium in the cellular structure. In addition, nanoscale secondary ion mass spectrometry (NanoSIMS) analysis of the 13C/12C ratio in pyrenoid and starch granules revealed the origin of carbon sources. The fraction of carbon in starch originating from CO2 decreased from 73 to 39% during cadmium stress. For the first time, the complementary use of high‐resolution elemental and isotopic imaging techniques allowed relating the impact of cadmium at the subcellular level with carbon assimilation in a mixotrophic microalga.

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Electron microscopy (EM) and nano secondary ion mass spectrometry (NanoSIMS) aim to acquiring nanometric information, which also imply ultraresolution and therefore these techniques require the best preservation of samples. Analytical techniques such as X‐ray spectroscopy and NanoSIMS are able to identify, localize and quantify chemical elements both at the whole cell and at the intracellular level. These techniques can be coupled with biological structural analysis. The goal in sample preparation is to maintain chemical elements at their original localization site as well as at their physiological active site. Therefore, sample preparation has to prevent also delocalization of the biological molecules (e.g. proteins, lipids). In EM and NanoSIMS, samples are subjected to drastic conditions such as high vacuum and beam energy. Thus, due to the characteristics of these devices, analyses are incompatible with native biological systems. Moreover, these techniques require thin sections of samples (TEM/X‐EDS (70‐100nm) and NanoSIMS (200‐300nm)). The sample should not be destroyed too quickly under the beam or by vacuum sublimation and must be stable chemically. Diffusible elements are quickly lost during dehydration and embedding step used for the routine preparation of biological specimens and so these methods can only be used if it is already known that the elements of interest are tightly bound. Sample preparation for EM and NanoSIMS must immobilize the biological elements, must eliminate water and must allow sectioning of the sample. As generally accepted in the literature, cryofixation by high pressure freezing followed by cryosubstitution are the best methods to limit redistribution of metal ions. In general, the preparation of biological samples for TEM and NanoSIMS is rather similar. Therefore, both techniques can be easily applied together and in a complementary way for bioimaging. In this work, different biological sample preparation techniques will be presented. The goal is to compare several cryomethods like cryosubstitution with different resins or freeze‐drying. An advanced sample preparation protocol was developed basing on high pressure freezing cryofixation follow by cryosubstitution or freeze‐drying, in order to limit metal redistribution, and preparation of adjacent ultramicrotome sections for parallel TEM and NanoSIMS analyses of the same cell. Best results were obtained by correlative imaging of a single cell by TEM and NanoSIMS combining the advantages of both techniques. As an illustration, the ultrastructure of a C. reinhardtii cell (Fig. 2) could be directly related to the spatial distribution of macro and trace elements present at basal levels in the cell (Figs. 1 and 3). Thus, metals could be localized in different cell organelles such as the pyrenoid and granules. For another example, epidermal cells on adherent culture (keratinocytes), localization of elements (e.g. Ni) demonstrates the importance of sample preparation. Correlative TEM and NanoSIMS shows potential for many future applications of subcellular imaging of trace elements in medicine and biology.