Matrix‐enhanced secondary ion mass spectrometry: the influence of MALDI matrices on molecular ion yields of thin organic films

In this work the effect in secondary ion mass spectrometry (SIMS) of several frequently used matrix‐assisted laser desorption/ionisation (MALDI) matrices on the secondary ion intensities of low molecular weight (m/z 400–800) organic dyes and a pharmaceutical is tested. Matrix (10^?1 M) and analyte (10^?2 M) solutions were made in methanol. Mixtures with several concentration ratios were prepared from these solutions and spincoated on Si substrates prior to time‐of‐flight (TOF)‐SIMS analysis. In some cases the presence of the MALDI matrices caused a considerable increase in the positive secondary (protonated) molecular ion signals. Enhancements of a factor of 20 and more were recorded. Generally, of the matrices used, 2,5‐dihydroxybenzoic acid and 2,4,6‐trihydroxyacetophenone brought about the highest intensity increases. It was also shown that matrix‐enhanced (ME‐)SIMS is capable of lowering the detection limits for molecule ions. However, the enhancement effect is strongly influenced by the analyte/matrix combination and its concentration ratio. As a result, finding an optimal analyte/matrix mixture can be a very time‐consuming process. Mostly, the presence of the matrices causes changes in the relative ion intensities in the TOF‐S‐SIMS spectra. Compared to the spectra recorded from samples without matrices, only a few additional peaks, such as signals that originate directly from the applied matrix or adduct ions, are observed in the mass spectra. Sometimes molecule ions and some characteristic fragments at high m/z values, that cannot be recorded without matrix, do appear in the spectrum when a matrix is present. In the negative mode no enhancement effect is observed on applying the studied MALDI matrices. The results obtained from samples treated with MALDI matrices are also compared to SIMS results for the same samples after Ag and Au metallisation (MetA‐SIMS). For three of the four tested compounds Au MetA‐SIMS resulted in higher ion yields than ME‐SIMS. For both techniques possible mechanisms that can account for the enhancement effect are proposed. Copyright © 2005 John Wiley & Sons, Ltd.     

New MALDI matrices based on lithium salts for the analysis of hydrocarbons and wax esters

Lithium salts of organic aromatic acids (lithium benzoate, lithium salicylate, lithium vanillate, lithium 2,5‐dimethoxybenzoate, lithium 2,5‐dihydroxyterephthalate, lithium α‐cyano‐4‐hydroxycinnamate and lithium sinapate) were synthesized and tested as potential matrices for the matrix‐assisted laser desorption/ionization (MALDI)‐mass spectrometry analysis of hydrocarbons and wax esters. The analytes were desorbed using nitrogen laser (337.1 nm) and ionized via the attachment of a lithium cation, yielding [M + Li]⁺ adducts. The sample preparation and the experimental conditions were optimized for each matrix using stearyl behenate and n‐triacontane standards. The performance of the new matrices in terms of signal intensity and reproducibility, the mass range occupied by matrix ions and the laser power threshold were studied and compared with a previously recommended lithium 2,5‐dihydroxybenzoate matrix (LiDHB) (Cva?ka and Svato?, Rapid Commun. Mass Spectrom. 2003, 17, 2203). Several of the new matrices performed better than LiDHB. Lithium vanillate offered a 2–3 times and 7–9 times higher signal for wax esters and hydrocarbons, respectively. Also, the signal reproducibility improved substantially, making this matrix a suitable candidate for imaging applications. In addition, the diffuse reflectance spectra and solubility of the synthesized compounds were investigated and discussed with respect to the compound's ability to serve as MALDI matrices. The applicability of selected matrices was tested on natural samples of wax esters and hydrocarbons. Copyright © 2014 John Wiley & Sons, Ltd.     

Matrix‐less laser desorption/ionisation mass spectrometry of polyphenols in red wine

Matrix‐assisted laser desorption/ionisation (MALDI) of small molecules is challenging and in most cases impossible due to interferences from matrix ions precluding analysis of molecules <300–500 Da. A common matrix such as ferulic acid belongs to an important class of compounds associated with antioxidant activity. If the shared phenolic structure is related to the propensity as an active MALDI matrix then it follows that direct laser desorption/ionisation should be possible for polyphenols. Indeed matrix‐less laser desorption/ionisation mass spectrometry is achieved whereby the analyte functions as a matrix and was used to monitor low molecular weight compounds in wine samples. Sensitivity ranging from 0.12–87 pmol/spot was achieved for eight phenolic acids (4‐coumaric, 4‐hydroxybenzoic, caffeic, ferulic, gallic, protocatechuic, syringic, vanillic) and 0.02 pmol/spot for trans‐resveratrol. Additionally, 4‐coumaric, 4‐hydroxybenzoic, caffeic, ferulic, gallic, syringic, vanillic acids and trans‐resveratrol were identified in wine samples using accurate mass measurements consistent with reported profiles based on liquid chromatography (LC)/MS. Minimal sample pre‐treatment make the technique potentially appropriate for fingerprinting, screening and quality control of wine samples. Copyright © 2009 John Wiley & Sons, Ltd.     

Comparative study of matrices for their use in the rapid screening of anabolic steroids by matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry

New data on sample preparation and matrix selection for the fast screening of androgenic anabolic steroids (AAS) by matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) is presented. The rapid screening of 15 steroids included in the World Anti‐Doping Agency (WADA) prohibited list using MALDI was evaluated. Nine organic and two inorganic matrices were assessed in order to determine the best matrix for steroid identification in terms of ionisation yield and interference by characteristic matrix ions. The best results were achieved for the organic matrices 2‐(4‐hydroxyphenylazo)benzoic acid (HABA) and trans‐3‐indoleacrylic acid (IAA). Good signals for all the steroids studied were obtained for concentrations as low as 0.010 and 0.050 µg/mL on the MALDI sample plate for the HABA and IAA matrices, respectively. For these two matrices, the sensitivity achieved by MALDI is comparable with the sensitivity achieved by gas chromatography/mass spectrometry (GC/MS), which is the conventional technique used for AAS detection. Furthermore, the accuracy and precision obtained with MALDI are very good, since an internal mass calibration is performed with the matrix ions. For the inorganic matrices, laser fluences higher than those used with organic matrices are required to obtain good MALDI signals. When inorganic matrices were used in combination with glycerol as a dispersing agent, an important reduction of the background noise was observed. Urine samples spiked with the study compounds were processed by solid‐phase extraction (SPE) and the screening was consistently positive. Copyright © 2009 John Wiley & Sons, Ltd.     

Identification of carbohydrates by matrix-free material-enhanced laser desorption/ionisation mass spectrometry

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) is a sensitive mass spectrometric technique which utilises acidic materials as matrices for laser energy absorption, desorption and ionisation of analytes. These matrix materials produce background signals particularly in the low-mass range and make the detection and identification of small molecules difficult and nearly impossible. To overcome this problem this paper introduces matrix-free material-enhanced laser desorption/ionisation mass spectrometry (mf-MELDI-MS) for the screening and analysis of small molecules such as carbohydrates. For this purpose, 4,4'-azo-dianiline was immobilised on silica gel enabling the absorption of laser energy sufficient for successful desorption and ionisation of low molecular weight compounds. The particle and pore sizes, the solvent system for suspension and the sample preparation procedures have been optimised. The newly synthesised MELDI material delivered excellent spectra with regard to signal-to-noise ratio and detection sensitivity. Finally, wheat straw degradation products and Salix alba L. plant extracts were analysed proving the high performance and excellent behaviour of the introduced material.     

Application of microbial alkaloid prodigiosin as a potent matrix for the MALDI mass spectrometry analysis of low-molecular-weight plant antioxidants

Microbial alkaloid prodigiosin is proposed as a new effective matrix for the analysis of low-molecular- weight plant antioxidants by MALDI mass spectrometry in the negative ion detection mode. It is demonstrated that the physicochemical characteristics of prodigiosin, such as ability to activate ionization/ desorption of analyte, high absorption coefficient at the working wavelengths of lasers, good solubility in solvents used for analytes, uniformity of crystallization on the target, stability under working conditions, and the absence of interfering peaks of fragment and cluster ions, are consistent with the recommendations for effective matrices. Prodigiosin as a matrix ensures the high-resolution detection of various plant antioxidants in complex mixtures. The obtained mass spectra of flavonoid aglycones were characterized by high quality (signal-to-noise ratio higher than 10³) and reproducibility. The use of prodigiosin for analyzing a complex preparation of plant antioxidants ensures the simultaneous recording and interpretation of more than two dozens of ions corresponding to various antioxidants with the molecular weights of 100–500 Da.     

The improved performance of MALDI‐TOF MS on the analysis of herbal saponins by using DHB‐GO composite matrix

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is an excellent analytical technique for rapid analysis of a variety of molecules with straightforward sample pretreatment. The performance of MALDI‐TOF MS is largely dependent on matrix type, and the development of novel MALDI matrices has aroused wide interest. Herein, we devoted to seek more robust MALDI matrix for herbal saponins than previous reported, and ginsenoside Rb1, Re, and notoginsenoside R1 were used as model saponins. At the beginning of the present study, 2,5‐dihydroxybenzoic acid (DHB) was found to provide the highest intensity for saponins in four conventional MALDI matrices, yet the heterogeneous cocrystallization of DHB with analytes made signal acquisition somewhat “hit and miss.” Then, graphene oxide (GO) was proposed as an auxiliary matrix to improve the uniformity of DHB crystallization due to its monolayer structure and good dispersion, which could result in much better shot‐to‐shot and spot‐to‐spot reproducibility of saponin analysis. The satisfactory precision further demonstrated that minute quantities of GO (0.1 μg/spot) could greatly reduce the risk of instrument contamination caused by GO detachment from the MALDI target plate under vacuum. More importantly, the sensitivity and linearity of the standard curve for saponins were improved markedly by DHB‐GO composite matrix. Finally, the application of detecting the Rb1 in complex biological sample was exploited in rat plasma and proved it applicable for pharmacokinetic study quickly. This work not only opens a new field for applications of DHB‐GO in herbal saponin analysis but also offers new ideas for the development of composite matrices to improve MALDI MS performance.     

一些含锗有机酸的快原子轰击质谱

本文报道了一系列含锗有机酸在甘油中的快原子轰击质谱（ＦＡＢＭＳ）及共在间硝基苄醇（ＮＢＡ）中的正、负离子ＦＡＢＭＳ。这些含锗有机酸在不同的底物中的ＦＡＢＭＳ显示了不同的特征。负离子谱提供了分子量信息，正、负离子谱可为这类化合物的结构鉴定提供互相补充的信息。讨论了底物和取代基对ＦＡＢＭＳ的影响，正、负离子的产生机制及离子的亚稳分解途径。     

MALDI Matrices for the Analysis of Low Molecular Weight Compounds: Rational Design,Challenges and Perspectives

The analysis of low molecular weight (LMW) compounds is of great interest to detect small pharmaceutical drugs rapidly and sensitively, or to trace and understand metabolic pathways. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) plays a central role in the analysis of high molecular weight (bio)molecules. However, its application for LMW compounds is restricted by spectral interferences in the low m/z region, which are produced by conventional organic matrices. Several strategies regarding sample preparation have been investigated to overcome this problem. A different rationale is centred on developing new matrices which not only meet the fundamental requirements of good absorption and high ionization efficiency, but are also vacuum stable and “MALDI silent”, i. e., do not give matrix-related signals in the LMW area. This review gives an overview on the rational design strategies used to develop matrix systems for the analysis of LMW compounds, focusing on (i) the modification of well-known matrices, (ii) the search for high molecular weight matrices, (iii) the development of binary, hybrid and nanomaterial-based matrices, (iv) the advance of reactive matrices and (v) the progress made regarding matrices for negative or dual polarity mode.     

Qualitative and quantitative analysis of low molecular weight compounds by ultraviolet matrix-assisted laser desorption/ionization mass spectrometry using ionic liquid matrices

A major problem hampering the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for quantitative measurements is the inhomogeneous distribution of analytes and matrices in solid sample preparations. The use of ionic liquids as matrices for the qualitative and quantitative analysis of low molecular weight compounds like amino acids, sugars and vitamins was investigated. The ionic liquid matrices are composed of equimolar combinations of classical MALDI matrices (sinapinic acid, alpha-cyano-4-hydroxycinnamic acid or 2,5-dihydroxybenzoic acid) with organic bases. These matrix systems allow a homogenous sample preparation with a thin ionic liquid layer having negligible vapour pressure. This leads to a facilitated qualitative and quantitative measurement of the analytes compared with classical solid matrices.     

Analysis of three different types of fullerene derivatives by laser desorption/ionization time‐of‐flight mass spectrometry with new matrices

Three different types of fullerene derivatives, namely methano[60]fullerene dicarboxylate esters, [60]fulleropyrrolidines, and imino[60]fullerenes, were analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry using trans‐4‐tert‐butyl‐4′‐nitrostilbene (TBNS), 1,8,9‐anthracenetriol (dithranol), 6‐aza‐2‐thiothymine (ATT), 2,5‐dihydroxybenzoic acid (DHB) and carbazole as matrices. Unit mass resolution (sufficient to clearly resolve isotopic peaks), high signal‐to‐noise ratio, and clean mass spectra for all analytes were acquired by the optimization of experimental parameters and choice of optimal solvent for the matrix and molar matrix‐to‐analyte ratio. The new matrix, TBNS, gave the best results in the positive‐ion mode, as it can provide higher yields of analyte molecular ions at a lower laser threshold than the other four matrices, together with a very low degree of unwanted fragmentations. In the negative‐ion mode dithranol was better than TBNS, and the other three matrices gave relatively poor mass spectra for these fullerene derivatives. Copyright © 2005 John Wiley & Sons, Ltd.     

分子烙印固相萃取技术在环境样品分析中的应用

分子烙印固相萃取技术克服了传统固相萃取技术选择性差的缺陷,实现了对复杂样品中特定分析对象或杂质的选择性提取,从而大大提高了分析测试的精度和准确性,并降低了检测限。该文对分子烙印聚合物(MIPs)作为固相萃取填料从复杂的环境样品中分离、富集和纯化微量及痕量的目标化合物进行了综述,涉及的目标化合物包括杀虫剂、除草剂、兽药等各类农药残留以及重金属离子和某些生物毒素等。     

Titanium dioxide anatase as matrix for matrix-assisted laser desorption/ionization analysis of small molecules

The use of inorganic species as assisting materials in matrix-assisted laser desorption/ionization (MALDI) analysis is an alternative approach to avoid interfering matrix ions in the low-mass region of the mass spectra. Reports of the application of inorganic species as matrices in MALDI analysis of small molecules are, however, scarce. Nevertheless, titanium dioxide (TiO(2)) powder has been reported to be a promising matrix medium. In this study we further explore the use of TiO(2) as a matrix for the MALDI analysis of low molecular weight compounds. We present results showing that nanosized TiO(2) anatase and TiO(2) rutile perform better as MALDI matrices than a commercial TiO(2) anatase/rutile mixture. Moreover, when using nanosized TiO(2) anatase as a matrix, high-quality mass spectra can be obtained with strong analyte signals and weak or non-existing matrix interference ions. Furthermore, our results show that the phase type plays an important role in the application of TiO(2) as a MALDI matrix.     

Characterization of humic substances by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and laser desorption/ionization (LDI-)TOFMS have been used to characterize Suwannee River humic substances, obtained from the International Humic Substances Society (IHSS), and Armadale soil fulvic acid (ASFA). An array of MALDI matrices were tested for use with humic substances, including alpha-cyano-4-hydroxycinammic acid (CHCA), 2-(4-hydroxyphenylazo)benzoic acid (HABA), 2,5-dihydroxybenzoic acid (DHBA), sinapinic acid, dithranol and norharmane. DHBA yielded the best results, exhibiting superior ionization efficiency, low noise, broad applicability to the analytes of interest, and most importantly producing an abundance of high mass ions, the highest observed being m/z 1848. A number of sample preparation modes were investigated; the overlayer method improved sample/matrix homogeneity and hence shot-to-shot reproducibility. The choice of the matrix, mass ratio of analyte to matrix, and the sample preparation protocol, were found to be the most critical factors governing the quality of the mass spectra. Matrix suppression was greatly enhanced by ensuring good mixing of matrix and analyte in the solid phase, proper optimization of the matrix/analyte ratio, and optimizing delayed extraction to ensure complete matrix-analyte reaction in the plume before ions are moved to the flight tube. A number of common features, in particular specific ions which could not be attributed to the matrices or to contaminants, were present in the spectra of all the humic substances, regardless of origin or operational definition. Additionally, a prominent repeating pattern of peaks separated by 55, 114 and 169 Da was clearly observed in both LDI and MALDI, suggesting that the humic compounds studied here may have quasi-polymeric or oligomeric features.     

Formation of M+. ions under matrix fast atom bombardment conditions: Does charge exchange reaction occur?

The formation of molecular ions, M^+., under fast atom bombardment (FAB) conditions using a liquid matrix was examined by using a new type of synthesized compounds in which preferential M^+. peaks appear in their FAB spectra. The FAB spectra were compared with the corresponding mass spectra obtained by the electron impact (EI) ionization, chemical ionization (CI) and charge-exchange ionization (CEI) methods. All of the spectra showed preferential peaks of M^+. ion and a characteristic intense fragment ion peak originating from a β-fission. The FAB spectra were similar in the fragment ions appearing in the EI spectra and were very similar in the fragmentation pattern to the CEI spectra using Ar^+. and Xe^+. as the reagent ions. Further, the FAB spectra did not show any doubly charged ion peaks, while the 70 eV EI spectra showed the peaks of doubly charged molecular and/or fragment ions. The isobutane CI spectra of the synthesized compounds suggested that the formation of M^+. ions occurred through the CE reaction with isobutane ion, C₄H₁₀^+., and the CI spectra showed a marked intense fragment ion peak originating from the β-fission which seemed to occur characteristically in CEI processes. The results obtained suggested that the formation of M^+. ions under matrix FAB conditions occurred mainly by CE reactions between the analytes M and matrix molecular ions B^+. and/or fragment ions b^+..     

Thermally annealed gold nanoparticles for surface-assisted laser desorption ionisation–mass spectrometry of low molecular weight analytes

Metal nanomaterials have an emerging role in surface-assisted laser desorption ionisation-mass spectrometry (SALDI-MS) providing a useful tool to overcome some limitations intrinsically related to the use of conventional organic matrices in matrix-assisted LDI-MS. In this contribution, the possibility to use a stainless-steel-supported gold nanoparticle (AuNP) film as a versatile platform for SALDI-MS was assessed. A sacrificial anode electrosynthetic route was chosen in order to obtain morphologically controlled core-shell AuNPs; the colloidal AuNPs were, thereafter, drop cast onto a stainless-steel sample plate and the resulting AuNP film was thermally annealed in order to improve its effectiveness as LDI-MS promoter. Spectroscopic characterization of the nanostructured film by X-ray photoelectron spectroscopy was crucial for understanding how annealing induced changes in the surface chemistry and influenced the performance of AuNPs as desorption/ionisation promoter. In particular, it was demonstrated that the post-deposition treatments were essential to enhance the AuNP core/analyte interaction, thus resulting in SALDI-MS spectra of significantly improved quality. The AuNP films were applied to the detection of three different classes of low molecular weight (LMW) analytes, i.e. amino acids, peptides and LMW polymers, in order to demonstrate the versatility of this nanostructured material.     

Analysis of low molecular weight compounds using MALDI‐ and LDI‐TOF‐MS: Direct detection of active pharmaceutical ingredients in different formulations

Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) is a high throughput, easy to use analytical technique. The simple sample preparation of this technique and its tolerance to the presence of contaminants are among its advantages. In contrast, depending on the matrix used, MALDI can ionize and generates ions in the low m /z range that complicate the interpretation of the spectra of low molecular weight compounds. To address this issue, one can envisage the use of tunable ionic matrices that can reduce the low m /z interferents. In this work, the ionic matrices triethylammonium α‐cyano‐4‐hydroxycinnamate and diisopropylammonium α‐cyano‐4‐hydroxycinnamate were used to directly analyze 14 pharmaceutical drugs in different formulations (coated tablets, noncoated tablets, capsules, and solutions). This methodology enabled the detection of their active compounds with minimum sample preparation, thus providing a straightforward approach for the forensic analysis of pharmaceutical drugs in the quest for detecting counterfeits. LDI‐MS experiments were also performed, and the active ingredient in all of the medicines analyzed were detected. However, MALDI‐MS spectra for the medicines analyzed herein showed less or no fragmentation than LDI‐MS, which makes the analysis easier.     

Microwave-assisted solvent extraction of solid matrices and subsequent detection of pharmaceuticals and personal care products (PPCPs) using gas chromatography-mass spectrometry

Concentrations of pharmaceuticals and personal care products (PPCPs) in natural solids remain largely unknown. Contributing to this, is a lack of methods permitting the simultaneous detection of the diverse, low-level contaminants present in these complex matrices. We have developed a microwave-assisted solvent extraction (MASE)-based method targeting seven diverse PPCPs (caffeine, 17β-estradiol, ibuprofen, ketoprofen, musk ketone, naproxen, and triclosan) and a molecular marker for fecal waste (epicoprostanol). The method consisted of optimizing the following variables: derivatization of the polar target analytes, silica gel open column clean-up, and gas chromatographic-mass spectrometric (GC-MS) analysis of sample extracts for analysis and detection of the compounds noted above. Testing of the method on spiked soil allowed for 89.6 ± 2.89% recovery of three target compounds and 25.0 ± 1.93% recovery of five of the compounds. Although the latter recoveries were low, the precision across all recoveries was high, suggesting good reproducibility in application of the method. Furthermore, we suspect that matrix effects are likely responsible for the lower recoveries. Techniques with the exclusive incorporation of organic solvents were found inapplicable in the study of a pharmaceutical salt, diphenhydramine HCl. Application of the developed method to sediment collected directly downstream of the effluent pipe of a wastewater treatment plant allowed detection of ibuprofen, naproxen, ketoprofen, and epicoprostanol at ng-μg per gram dry weight concentrations. The observation of acidic pharmaceuticals, previously believed to exhibit insignificant sorption to solid matrices, in the tested sediment samples, coupled with application of biosolids for agricultural purposes, demonstrates the need for expanded investigation of PPCP contamination of natural solid matrices.     

Static secondary ion mass spectrometry for organic and inorganic molecular analysis in solids

The use of mass spectra in secondary ion mass spectrometry (S-SIMS) to characterise the molecular composition of inorganic and organic analytes at the surface of solid samples is investigated. Methodological aspects such as mass resolution, mass accuracy, precision and accuracy of isotope abundance measurements, influence of electron flooding and sample morphology are addressed to assess the possibilities and limitations that the methodology can offer to support the structural assignment of the detected ions. The in-sample and between-sample reproducibility of relative peak intensities under optimised conditions is within 10%, but experimental conditions and local hydration, oxidation or contamination can drastically affect the mass spectra. As a result, the use of fingerprinting for identification becomes compromised. Therefore, the preferred way of interpretation becomes the deductive structural approach, based on the use of the empirical desorption–ionisation model. This approach is shown to allow the molecular composition of inorganic and organic components at the surface of solids to be characterised. Examples of inorganic speciation and identification of organic additives with unknown composition in inorganic salt mixtures are given. The methodology is discussed in terms of foreseen developments with respect to the use of polyatomic primary ions.     

Spectral characterisation of eight glycerolipids and their detection in natural samples using time‐of‐flight secondary ion mass spectrometry

In recent years, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) with cluster ion sources has opened new perspectives for the analysis of lipid biomarkers in geobiology and organic geochemistry. However, published ToF‐SIMS reference spectra of relevant compounds are still sparse, and the influence of the chemical environment (matrix) on the ionisation of molecules and their fragmentation is still not well explored. This study presents ToF‐SIMS spectra of eight glycerolipids as common target compounds in biomarker studies, namely ester‐ and ether‐bound phosphatidylethanolamine, ester‐ and ether‐bound phosphatidylcholine, ester‐bound phosphatidylglycerol, ester‐ and ether‐bound diglycerides and archaeol, obtained with a Bi cluster ion source. For all of these compounds, the spectra obtained in positive and negative analytical modes showed characteristic fragments that could clearly be assigned to e.g. molecular ions, functional groups and alkyl chains. By comparison with the reference spectra, it was possible to track some of these lipids in a pre‐characterised organic extract and in cryosections of microbial mats. The results highlight the potential of ToF‐SIMS for the laterally resolved analysis of organic biomarkers in environmental materials. The identification of the target compounds, however, may be hampered by matrix effects (e.g. adduct formation) and often require careful consideration of all spectral features and taking advantage of the molecular imaging capability of ToF‐SIMS. Copyright © 2009 John Wiley & Sons, Ltd.