MALDI ionization: the role of in-plume processes

Direct sub-atmospheric pressure ionization mass spectrometry: Evaporation/sublimation-driven ionization is amazing, fundamentally, and practically

This paper covers direct sub-atmospheric pressure ionization mass spectrometry (MS). The discovery, applications, and mechanistic aspects of novel ionization processes for use in MS that are not based on the high-energy input from voltage, laser, and/or high temperature but on sublimation/evaporation within a region linking a higher to lower pressure and modulated by heat and collisions, are discussed, including how this new reality has guided a series of discoveries, instrument developments, and commercialization. A research focus, inter alia, is on how best to understand, improve, and use these novel ionization processes, which convert volatile and nonvolatile compounds from solids (sublimation) or liquids (evaporation) into gas-phase ions for analysis by MS providing reproducible, accurate, sensitive, and prompt results. Our perception on how these unprecedented versus traditional ionization processes/methods relate to each other, how they can be made to coexist on the same mass spectrometer, and an outlook on new and expanded applications (e.g., clinical, portable, fast, safe, and autonomous) is presented, and is based on ST's Opening lecture presentation at the Nordic Mass spectrometry Conference, Geilo, Norway, January 2023. Focus will be on matrix-assisted ionization (MAI) and solvent-assisted ionization (SAI) MS covering the period from 2010 to 2023; a potential paradigm shift in the making.

Negative-Ion Electron Capture Dissociation of MALDI-Generated Peptide Anions

Negative-ion electron capture dissociation (niECD) is an anion MS/MS technique that provides fragmentation analogous to conventional ECD, including high peptide sequence coverage and retention of labile post-translational modifications (PTMs). niECD has been proposed to be the most efficient for salt-bridged zwitterionic precursor ion structures. Several important PTMs, e.g., sulfation and phosphorylation, are acidic and can, therefore, be challenging to characterize in the positive-ion mode. Furthermore, PTM-friendly techniques, such as ECD, require multiple precursor ion-positive charges. By contrast, singly charged ions, refractory to ECD, are most compatible with niECD. Because electrospray ionization (ESI) typically yields multiply charged ions, we sought to explore matrix-assisted laser desorption/ionization (MALDI) in combination with niECD. However, the requirement for zwitterionic gaseous structures may preclude efficient niECD of MALDI-generated anions. Unexpectedly, we found that niECD of anions from MALDI is not only possible but proceeds with similar or higher efficiency compared with ESI-generated anions. Matrix selection did not appear to have a major effect. With MALDI, niECD is demonstrated up to m/z ∼4300. For such larger analytes, multiple electron captures are observed, resulting in triply charged fragments from singly charged precursor ions. Such charge-increased fragments show improved detectability. Furthermore, significantly improved (∼20-fold signal-to-noise increase) niECD spectral quality is achieved with equivalent sample amounts from MALDI vs ESI. Overall, the reported combination with MALDI significantly boosts the analytical utility of niECD.

Effect of Counterions on the Soft Ionization Mass Spectra of Analytes with Multiple Permanent Charges

Multiply permanently charged analytes (MPCAs) are of great interest for various applications. MPCA soft ionization mass spectra (MS) strongly depend on the counterions of MPCA. We have studied thoroughly this effect to expand the use of MS in MPCA characterization. To this end, β-cyclodextrin-based MPCAs with 7 (MIM7NBCD) and 14 (MIM14BCD) quaternary ammonium charges with a series of monovalent counterions were prepared and their MS were measured using two of the most popular soft ionization techniques, electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). MALDI MS of both analytes were well resolved, with signals assignable to the analytes only with the two least basic tested counterions (ClO4- and TfO-). Similarly, analyte-assignable signals were observed in ESI MS of MIM14BCD only with ClO4- and TfO-. The situation was opposite with ESI MS of MIM7NBCD where assignable signals were observed with Cl- but not with TfO-. Thus, to get high-quality MS, binding between the MPCA permanent charges and the counterions must be of the optimal effective strength, given also by the number of analyte permanent charges as shown by the simple combinatorial model of binding. Of practical interest is the observation that unsuitable counterions can be replaced in situ by an excess of corresponding acid. The findings form a coherent framework for interpreting and improving MPCA mass spectra.

Quantitative mass spectrometry imaging (qMSI): A tutorial

Mass spectrometry imaging (MSI) is an analytical technique that enables the simultaneous detection of hundreds to thousands of chemical species while retaining their spatial information; usually, MSI is applied to biological tissues. Combining these elements can create ion images, which allows for the identification and localization of multiple chemical species within the sample. Being able to produce molecular images of biological tissues has already impacted the study of health and disease; however, the next logical step is being able to combine MSI with quantitative mass spectrometry methods to both quantify and determine the localization of disease progression or drug action. In this tutorial, we will detail the main factors to consider when designing a qMSI experiment and highlight the methods that have been developed to overcome these added complexities, specifically for those newer to the field of MSI.

Nitro Indole Derivatives as Novel Dual-Polarity Matrices for MALDI Mass Spectrometry and Imaging with Broad Applications

A new matrix framework is presented in this study for the improved ionization efficiency of complex mixtures by matrix-assisted laser desorption ionization (MALDI) mass spectrometry/imaging. Five nitro indole (NI) derivatives [3-methyl-4-nitro-1H-indole (3,4-MNI), 3-methyl-6-nitro-1H-indole (3,6-MNI), 2,3-dimethyl-4-nitro-1H-indole (2,3,4-DMNI), 2,3-dimethyl-6-nitro-1H-indole (2,3,6-DMNI), and 4-nitro-1H-indole (4-NI)] were synthesized and shown to produce both positive and negative ions with a broad class of analytes as MALDI matrices. NI matrices were compared to several common matrices, such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxylcinnamic acid (CHCA), sinapinic acid (SA), 1,5-diaminonaphthelene (1,5-DAN), and 9-aminoacridine (9-AA), for the analysis of lipid, peptide, protein, glycan, and perfluorooctanesulfonic acid (PFOS) compounds. 3,4-MNI demonstrated the best performance among the NI matrices. This matrix resulted in reduced ion suppression and better detection sensitivity for complex mixtures, for example, egg lipids/milk proteins/PFOS in tap water, while 2,3,6-DMNI was the best matrix for blueberry tissue imaging. Several important aspects of this work are reported: (1) dual-polarity ion production with NI matrices and complex mixtures; (2) quantitative analysis of PFOS with a LOQ of 0.5 ppb in tap water and 0.05 ppb in MQ water (without solid phase extraction enrichment), with accuracy and precision within 5%; (3) MALDI imaging with 2,3,6-DMNI as a matrix for plant metabolite/lipid identification with ionization enhancement in the negative ion mode m/z 600-900 region; and (4) development of a thin film deposition under/above tissue method for MALDI imaging with a vacuum sublimation matrix on a high-vacuum MALDI instrument.

Proteomics for Microalgae Extracts by High-Resolution Mass Spectrometry

Two protocols of protein extraction from Arthrospira platensis (spirulina) microalgae to study their proteome by mass spectrometry (MS) are here presented. The first is based on an aqueous buffer solution of Tris-HCl and the second on cold acetone. The identification of proteins was carried out by a bottom-up approach, which involves enzymatic digestion of extracted proteins followed by either matrix-assisted laser desorption ionization with time-of-flight (MALDI-TOF) MS or liquid chromatography (LC) coupled with electrospray ionization (ESI) and Fourier-transform tandem MS. While MALDI-TOF MS allowed for a fast peptide mass fingerprinting (PMF) check yet identifying less than 20 proteins in the extracted samples, the data-dependent acquisitions (DDA) mode of reversed-phase (RP) LC-ESI tandem FTMS/MS separations allowed us to recognize more than one hundred proteins by searching into dedicated spectral libraries. The application of MALDI-TOF MS analysis was found, however, of great support for preliminary investigations of cyanobacteria samples before proceeding with the RPLC-ESI-MS/MS DDA investigation, which definitively allows for a qualitative proteome analysis also of minor spirulina proteins in processed foodstuffs. Although the protein content in spirulina can be influenced by cultivation and environmental conditions, e.g., light intensity, climate, and water/air quality, here the qualitative chemical profiles of the examined samples were characterized by similar composition in high-quality proteins as phycocyanins and phycoerythrins.

Nanoparticle-based applications by atmospheric pressure matrix assisted desorption/ionization mass spectrometry

Recently, the development of atmospheric pressure matrix assisted desorption/ionization mass spectrometry (AP MALDI MS) has made contributions not only to biomolecule analysis but also to spatial distribution. This has positioned AP MALDI as a powerful tool in multiple domains, thanks to its comprehensive advantages compared to conventional MALDI MS. These developments have addressed challenges associated with previous AP MALDI analysis systems, such as optimization of apparatus settings, synthesis of novel matrices, preconcentration and isolation strategies before analysis. Herein, applications in different fields using AP MALDI MS were described, including peptide and protein analysis, metabolite analysis, pharmaceutical analysis, and mass spectrometry imaging.

Applications of MALDI-TOF-MS in structural characterization of synthetic polymers

In recent years, matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been utilized to rapidly and precisely characterize the detailed molecular structures of synthetic polymers. This review summarizes recent progress regarding MALDI-TOF-MS for the characterization of synthetic polymers with a focus on specific important experimental aspects including sample preparation, the choice of matrix, the effects of cationizing agents and solvents, data processing and various applications. Finally, the recent trend of MALDI-TOF-MS development is discussed. We hope this review will be instructive for graduate students and junior users who need to use MALDI-TOF-MS as a necessary characterization technique for new synthetic polymers.

A Caged In-Source Laser-Cleavable MALDI Matrix with High Vacuum Stability for Extended MALDI-MS Imaging

Insufficient vacuum stability of matrix chemicals is a major limitation in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) of large tissue sample cohorts. Here, we designed and synthesized the photo-cleavable caged molecule 4,5-dimethoxy-2-nitrobenzyl-2,5-dihydroxyacetophenone (DMNB-2,5-DHAP) and employed it for lipid MALDI-MSI of mouse brain tissue sections. DMNB-2,5-DHAP is vacuum-stable in a high vacuum MALDI ion source for at least 72 h. Investigation of the uncaging process suggested that the built-in laser (355 nm) in the MALDI ion source promoted the in situ generation of 2,5-DHAP. A caging group is used for the first time in designing a MALDI matrix that is vacuum-stable, uncaged upon laser irradiation during the measurement process, and that boosts lipid ion intensity with MALDI-2 laser-induced postionization.

Electron-transfer MALDI MS methodology for microalgae/phytoplankton pigments analysis

The method describes pigment analysis from microalgae/phytoplankton extracts using electron-transfer Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (ET MALDI MS). Current microalgae/phytoplankton pigment analysis requires resource- and time-intensive chromatographic methods due to the broad polarity range of the target analytes. On the other hand, traditional MALDI MS chlorophyll analysis, using proton-transfer matrices such as 2,5-dihydroxybenzoic acid (DHB) or α-cyano-4-hydroxycinnamic acid (CHCA), results in central metal loss and phytol-ester cleavage. ET MALDI MS is an alternative for the rapid screening and detection of pigments in microalgae extracts.•MALDI matrices with ionization energies above 8.0 eV guarantee electron-transfer processes from photosynthetic and photoprotective pigments whose ionization energies lay below 7.5 eV.•ET MALDI MS pigment analysis agrees with data gathered from conventional chromatographic techniques (HPLC) and optical microscopy for pigment extracts from C. vulgaris cultures and freshwater phytoplankton samples.•The ET MALDI MS method allows fast and reliable detection of pigments in microalgae cultures and freshwater phytoplankton samples.

Desorption and ablation regimes in UV-MALDI: the critical fluence

Although MALDI is a widely used technique, there is so far no theoretical description able to reproduce some critical aspects of the experimental results. For example, there is experimental as well as theoretical controversy regarding the minimum laser fluence, i.e., the so-called fluence threshold (F _T), required to evaporate a sample. Furthermore, although the different processes involved in ion production have been the focus of many investigations, the fact is that the primary process for ion formation in MALDI is not desorption but ablation. In this work, we present a new phenomenological approach for understanding MALDI results based on a simple, but physically intuitive, idea consisting of limiting the laser-matter interaction process to three layers. This description allows us to consider the different processes that dominate ion formation, i.e., heat dissipation, as well as the different existing regimes. Concretely, we present the results for three different matrices, i.e., DHB, ferulic acid (FA) and α-cyano-4-hydroxycinnamic acid (CHCA), in the limit of low fluence. The simulations we carried out show great qualitative and pseudo-quantitative agreement with the experimental results. Also, based on the simulation results, it is possible to distinguish clearly between the two dominant regimes, i.e., desorption and ablation, and it is possible, therefore, to estimate the critical fluence (F _C) that defines the transition from one regime to another.

Disentangle a Complex MALDI TOF Mass Spectrum of Polyethylene Glycols into Three Separate Spectra via Selective Formation of Protonated Ions and Sodium or Potassium Adducts

In MALDI TOF MS analysis, complicated mass spectra can usually be recorded for polymers with high affinities to protons and alkali metal ions. For these polymers, protonated ions and sodium and potassium adducts can often be formed concomitantly. By distributing these ions into three separate spectra of protonated ions, sodium adducts, and potassium adducts, significantly simplified spectra can be acquired. Mass spectra consisting of only sodium or potassium adducts can often be obtained by simply adding sodium salt and potassium salt, respectively. We report here a method to selectively generate protonated ions. A polyethylene glycol (PEG) sample with amino end groups was selected as the model polymer and α-cyano-4-hydroxycinnamic acid (CHCA) as the matrix. Octadecylamine (ODA) or a mixture of a tetrabutylammonium (TBA) salt and an ammonium salt was used as the co-matrix to inhibit the release of sodium and potassium ions and their related adducts into the MALDI gas phase plume. By depositing the polymer sample on top of a preloaded layer of CHCA with a co-matrix, the generation of Na⁺ and K⁺ adducts is suppressed, while [ODA + H]⁺ and NH₄⁺ released from the preloaded matrix layer can serve as protonation reagents to protonate the polymer molecules via proton transfer reactions. It is clearly demonstrated that disentangling a complex mass spectrum filled densely with various series of ions into three separate spectra, with each one consisting of only one type of ions, allows unambiguous identification of mass peaks and greatly helps the interpretation of MS results.

Laser-Shock-Driven In Situ Evolution of Atomic Defect and Piezoelectricity in Graphitic Carbon Nitride for the Ionization in Mass Spectrometry

Nanostructures─coupled with mass spectrometry─have been intensively investigated to improve the detection sensitivity and reproducibility of small biomolecules in laser desorption/ionization mass spectrometry (LDI-MS). However, the impact of laser-induced shock wave on the ionization of the nanostructures has rarely been reported. Herein, we systematically elucidate the laser shock wave effect on the ionization in terms of the in situ development of atomic defects and piezoelectricity in two-dimensional graphitic carbon nitride nanosheets (g-C₃N₄ NS) by short laser pulses. The mass analysis results of immunosuppressive drugs verify the enhanced LDI-MS performance, structurally originating from anisotropic lattice distortions in g-C₃N₄ NS, i.e., in-plane extension (contraction) and out-of-plane contraction (extension) that modulate the charge carrier motion. Along with the experimental investigations, density functional theory calculations on Mulliken charges and dipole moments demonstrate the contribution of defect and piezoelectricity to the ionization. The results of this study provide a mechanistic understanding of the underlying ionization processes, which is crucial for revealing the full potential of laser shock waves in LDI-MS.

Diagnosing, Typing, and Staging of Renal Cell Carcinoma by Designer Matrix-Based Urinary Metabolic Analysis

Molecular diagnosing, typing, and staging have been considered to be the ideal alternatives of imaging-based detection methods in clinics. Designer matrix-based analytical tools, with high speed, throughout, efficiency and low/noninvasiveness, have attracted much attention recently for in vitro metabolite detection. Herein, we develop an advanced metabolic analysis tool based on highly porous metal oxides derived from available metal-organic frameworks (MOFs), which elaborately inherit the morphology and porosity of MOFs and newly incorporate laser adsorption capacity of metal oxides. Through optimized conditions, direct high-quality fingerprinting spectra in 0.5 μL of urine are acquired. Using these fingerprinting spectra, we can discriminate the renal cell carcinoma (RCC) from healthy controls with higher than 0.99 of area under the curve (AUC) values (R²Y(cum) = 0.744, Q² (cum) = 0.880), as well, from patients with other tumors (R²Y(cum) = 0.748, Q²(cum) = 0.871). We also realize the typing of three RCC subtypes, including clear cell RCC, chromophobe RCC (R²Y(cum) = 0.620, Q²(cum) = 0.656), and the staging of RCC (R²Y(cum) = 0.755, Q²(cum) = 0.857). Moreover, the tumor sizes (threshold value is 3 cm) can be remarkably recognized by this advanced metabolic analysis tool (R²Y(cum) = 0.710, Q²(cum) = 0.787). Our work brings a bright prospect for designer matrix-based analytical tools in disease diagnosis, typing and staging.

Exosome Metabolic Patterns on Aptamer-Coupled Polymorphic Carbon for Precise Detection of Early Gastric Cancer

Gastric cancer (GC) presents high mortality worldwide because of delayed diagnosis. Currently, exosome-based liquid biopsy has been applied in diagnosis and monitoring of diseases including cancers, whereas disease detection based on exosomes at the metabolic level is rarely reported. Herein, the specific aptamer-coupled Au-decorated polymorphic carbon (CoMPC@Au-Apt) is constructed for the capture of urinary exosomes from early GC patients and healthy controls (HCs) and the subsequent exosome metabolic pattern profiling without extra elution process. Combining with machine learning algorithm on all exosome metabolic patterns, the early GC patients are excellently discriminated from HCs, with an accuracy of 100% for both the discovery set and blind test. Ulteriorly, three key metabolic features with clear identities are determined as a biomarker panel, obtaining a more than 90% diagnostic accuracy for early GC in the discovery set and validation set. Moreover, the change law of the key metabolic features along with GC development is revealed through making a comparison among HCs and GC at early stage and advanced stage, manifesting their monitoring ability toward GC. This work illustrates the high specificity of exosomes and the great prospective of exosome metabolic analysis in disease diagnosis and monitoring, which will promote exosome-driven precision medicine toward practical clinical application.

Metabolic Molecular Diagnosis of Inflammatory Bowel Disease by Synergistical Promotion of Layered Titania Nanosheets with Graphitized Carbon

Due to inefficient diagnostic methods, inflammatory bowel disease (IBD) normally progresses into severe complications including cancer. Highly efficient extraction and identification of metabolic fingerprints are of significance for disease surveillance. In this work, we synthesized a layered titania nanosheet doped with graphitized carbon (2D-GC-mTNS) through a simple one-step assembly process for assisting laser desorption ionization mass spectrometry (LDI-MS) for metabolite analysis. Based on the synergistic effect of graphitized carbon and mesoporous titania, 2D-GC-mTNS exhibits good extraction ability including high sensitivity (< 1 fmol µL^-1) and great repeatability toward metabolites. A total of 996 fingerprint spectra were collected from hundreds of native urine samples (including IBD patients and healthy controls), each of which contained 1220 m/z metabolite features. Diagnostic model was further established for precise discrimination of patients from healthy controls, with high area under the curve value of 0.972 and 0.981 toward discovery cohort and validation cohort, respectively. The 2D-GC-mTNS promotes LDI-MS to be close to clinical application, with rapid speed, minimum sample consumption and free of sample pretreatment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-022-00055-0.

Surface-assisted laser desorption/ionization mass spectrometry imaging: A review

In the last decades, surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) has attracted increasing interest due to its unique capabilities, achievable through the nanostructured substrates used to promote the analyte desorption/ionization. While the most widely recognized asset of SALDI-MS is the untargeted analysis of small molecules, this technique also offers the possibility of targeted approaches. In particular, the implementation of SALDI-MS imaging (SALDI-MSI), which is the focus of this review, opens up new opportunities. After a brief discussion of the nomenclature and the fundamental mechanisms associated with this technique, which are still highly controversial, the analytical strategies to perform SALDI-MSI are extensively discussed. Emphasis is placed on the sample preparation but also on the selection of the nanosubstrate (in terms of chemical composition and morphology) as well as its functionalization possibilities for the selective analysis of specific compounds in targeted approaches. Subsequently, some selected applications of SALDI-MSI in various fields (i.e., biomedical, biological, environmental, and forensic) are presented. The strengths and the remaining limitations of SALDI-MSI are finally summarized in the conclusion and some perspectives of this technique, which has a bright future, are proposed in this section.

Synthesis and Investigation of Novel CHCA-Derived Matrices for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of Lipids

A significant area of study and upgrading for increasing sensitivity and general performances of matrix-assisted laser-desorption ionization (MALDI) mass spectrometry (MS) is related to matrix design. Several efforts have been made to address the challenge of low-mass-region interference-free for metabolomics analysis and specifically for lipidomics. To this aim, rationally designed matrices as 4-chloro-α-cyanocinnamic acid (ClCCA) were introduced and reported to provide enhanced analytical performances. We have taken this rational design one step further by developing and optimizing new MALDI matrices with a range of modifications on the CHCA core, involving different functionalities and substituents. Of particular interest was the understanding of the electron-withdrawing (e.g., nitro-) or donating (e.g., methoxy-) effects along with the extent of conjugation on the ionization efficiency. In the present work, ten matrices were designed on a reasonable basis, synthesized, and characterized by NMR and UV spectroscopies and laser desorption ionization. With the assistance of these putative MALDI matrices, samples containing phospholipids (PL), and neutral di-/tri-acylglycerols (DAG, TAG) were investigated using milk, fish, blood, and human plasma extracts. In comparison with CHCA and ClCCA, four of them, viz. [(2E,4E)-2-cyano-5-(4-methoxyphenyl)penta-2,4-dienoic acid] (1), [(2E,4E)-2-cyano-5-(4-nitrophenyl)penta-2,4-dienoic acid] (2), [(E)-2-cyano-3-(6-methoxynaphthalen-2-yl)acrylic acid] (6) and [(E)-2-cyano-3-(naphthalen-2-yl)acrylic acid] (7) displayed good to even excellent performances as MALDI matrices in terms of ionization capability, interference-free spectra, S/N ratio, and reproducibility. Especially compound 7 (cyano naphthyl acrylic acid, CNAA) was the election matrix for PL analysis and matrix 2 (cyano nitrophenyl dienoic acid, CNDA) for neutral lipids such as DAG and TAG in positive ion mode.

Analysis of Gliricidia sepium Leaves by MALDI Mass Spectrometry Imaging

When investigating the potential use of plants as a raw material for an all-natural cosmetic formulation, the main parameters are the chemical composition, antioxidant potential, antimicrobial action, and toxicity. Additionally, the production of natural cosmetics should also consider the availability of primary materials and the environmental and socioeconomic impact. Gliricidia sepium is a species that produces a large amount of plant material, being cultivated in the agroforestry system. However, studies of phytochemical composition and chemical spatial distribution are scarcely using the MALDI MS (matrix-assisted laser desorption ionization mass spectrometry) and MALDI MSI (mass spectrometry imaging) techniques. A methodology was developed to optimize ionization parameters and analysis conditions by evaluating the efficiency of three matrices: α-cyano-4-hydroxycinnamic acid, 2,5-dihydroxybenzoic acid (DHB), and 2-mercaptobenzothiazole in MALDI MS analysis. All results were compared to ESI MS (electrospray ionization mass spectrometry), and afterward, MALDI MSI analysis was performed on the leaf surface. This study showed through phytochemical analysis that G. sepium leaves are composed of polyphenols and tannins, concluding that the methanolic extract had a higher amount of flavonoid content. Four compounds were identified on the leaf surface, and their spatial distribution was analyzed by MALDI MS using DHB as a matrix. Kaempferol, isorhamnetin, and some fatty acids showed potential applicability for cosmetical use. All the extracts presented antioxidant activity or antimicrobial action and no cytotoxicity. Therefore, extracts of G. sepium could be used as raw materials in cosmetics.

Mass Spectrometry of Au10(4-tert-butylbenzenethiolate)10 Nanoclusters Using Superconducting Tunnel Junction Cryodetection Reveals Distinct Metastable Fragmentation

Cryodetection mass spectrometry (MS) was used to study the Au₁₀(TBBT)₁₀ (TBBT = 4-tert-butylbenzenethiolate) catenane nanocluster. The matrix-assisted laser desorption ionization (MALDI) process generates distinct fragments that can be arranged into two distinct regimes: (i) in-source fragmentation, which occurs rapidly in a relatively short (<170 ns) time frame, and (ii) metastable fragmentation, which occurs postacceleration during a time-of-flight (TOF) mass analysis over a longer time frame (>170 ns-250 μs). Using MALDI-TOF MS with superconducting tunnel junction (STJ) cryodetection, distinct metastable nanocluster fragments were resolved at lower energies deposited into the detector. The results also demonstrated that STJ cryodetection MS can be used to acquire multiple (>10), simultaneous tandem mass spectra in a single experiment. Simulated fragmentation of the Au₁₀ nanocluster using ab initio molecular dynamics (AIMD) revealed the different fragmentation processes and confirmed the MS results. Using both the empirical MS data and AIMD calculations, fragmentation pathways are proposed for Au₁₀(TBBT)₁₀, which terminate with two small, stable ringed species.

The local electric field effect of onion-like carbon nanoparticles for improved laser desorption/ionization efficiency of saccharides

It is still a challenge to improve ionization efficiency of saccharides in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Herein, the highly curved onion-like carbon nanoparticles (OCS) were synthesized from the low-price candle raw via a facile strategy. The unique nanostructure of OCS showed large surface area with plentiful mesoporous architecture, highly curved sp² carbon with regulating electronic effect, and good hydrophilicity, which could be beneficial to facilitate the desorption and ionization efficiency in MS process. The prepared OCS material as MALDI matrix exhibited the superior performance for the detection of xylose, glucose, maltose monohydrate, and raffinose pentahydrate in positive-ion mode with low background noise, enhanced ion intensities, uniform distribution, excellent reproducibility, good salt-tolerance, and high sensitivity compared to control candle soot (CS) and traditional α-cyano-4-hydroxycinnamic acid (CHCA) matrices. This highly effective LDI of OCS matrix was attributed to its enhancing local electric field effect, strong UV absorption ability, and high photo-thermal conversion performance. Furthermore, the OCS-assisted LDI MS approach was employed to quantitatively detect glucose in rat serum. This LDI MS platform may have valuable for the analysis of metabolites in clinical research.

A new update of MALDI-TOF mass spectrometry in lipid research

Matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS) is an indispensable tool in modern lipid research since it is fast, sensitive, tolerates sample impurities and provides spectra without major analyte fragmentation. We will discuss some methodological aspects, the related ion-forming processes and the MALDI MS characteristics of the different lipid classes (with the focus on glycerophospholipids) and the progress, which was achieved during the last ten years. Particular attention will be given to quantitative aspects of MALDI MS since this is widely considered as the most serious drawback of the method. Although the detailed role of the matrix is not yet completely understood, it will be explicitly shown that the careful choice of the matrix is crucial (besides the careful evaluation of the positive and negative ion mass spectra) in order to be able to detect all lipid classes of interest. Two developments will be highlighted: spatially resolved Imaging MS is nowadays well established and the distribution of lipids in tissues merits increasing interest because lipids are readily detectable and represent ubiquitous compounds. It will also be shown that a combination of MALDI MS with thin-layer chromatography (TLC) enables a fast spatially resolved screening of an entire TLC plate which makes the method competitive with LC/MS.

Reactive Matrices for Analytical Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry

In recent years, a special focus is placed on the usage of reactive matrices for analytical matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Since 2003, when the term "reactive matrices" was suggested and the dignity of compounds, possessing dualistic properties as matrices and derivatization agents was demonstrated, corresponding approach has found application in various fields and, in particular, in bioanalysis (metabolomics, lipidomics, etc.). The main advantage of this methodology is that it reduces sample treatment time, simplifies the procedure of sample handling, improves the sensitivity of analysis, enhances the molecular identification and profiling. Within the framework of this review, the main attention is paid to "true" reactive matrices that interact with analyte molecules through an exchange or addition reactions. A special section discusses practical application of reactive matrices in the determination of the distribution of targeted and non-targeted organic substances on the surface of biological tissue sections by MALDI-MS imaging. In this critical review, a controversial proposal is made to consider protonating and deprotonating matrices as reactive, because they can undergo a chemical reaction such as proton transfer that occurs in both target solution and MALDI plume. In this respect, special attention is paid to "proton sponge" matrices that have found a wide application in the analysis of various acidic compounds by MALDI-MS in the negative mode. Historical data on the formation of ions and the fate of matrices in MALDI are considered at the beginning of this article.

Re-exploring α-Cyano-4-Hydroxycinnamic Acid as a Reactive Matrix for Selective Detection of Glutathione via MALDI-MS

Herein, we re-explored α-cyano-4-hydroxycinnamic acid (CHCA) as a reactive matrix for selective and sensitive analysis of glutathione (GSH) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). CHCA efficiently reacted with GSH, and the resulting CHCA-GSH conjugate was readily detected by MALDI-MS without interferences. The detection limit of the CHCA-GSH conjugate decreased to 200 pmol μL^-1, which was 2 orders of magnitude lower than that of pure GSH.Forapplication, CHCA was successfully applied for the detection of GSH, present in HepG2 cell lysates. The results demonstrated detection advantages of simple, high-throughput, and selective and screening of GSH in biological samples by MALDI-MS.

Design of Experiments for Matrix-Assisted Laser Desorption/Ionization of Amphiphilic Poly(Ethylene Oxide)-b-Polystyrene Block Copolymers

Matrix-assisted laser/desorption ionization (MALDI) has become a very popular ionization technique for mass spectrometry of synthetic polymers because it allows high throughput analysis of low amounts of sample while avoiding the complexity introduced by extensive multiple charging of electrospray ionization. Yet, fundamental mechanisms underlying this ionization process are not fully understood, so development of sample preparation methods remains empirical. Reliable prediction for the optimal matrix/analyte/salt system is indeed still not possible for homopolymers and it becomes even more challenging in the case of amphiphilic block copolymers where conditions dictated by one block are not compatible with MALDI requirements of the second block. In order to perform MALDI of copolymers composed of poly (ethylene oxide) (PEO) and polystyrene (PS) blocks, it was postulated here that experimental conditions suitable for both species would also be successful for PEO-b-PS. Accordingly, designs of experiments based on Quantitative Structure Activity Relationship (QSAR) analysis were first implemented, studying the influence of 19 matrices and 26 salts on the laser fluence requested for successful MALDI. This analysis first permitted to highlight correlations between the investigated 10 descriptors of matrices and salts and the analytical response, and then to construct models that permits reliable predictions of matrix/salt couples to be used for one or the other homopolymer. Selected couples were then used for MALDI of a PEO-b-PS copolymer but no general trend was observed: experimental conditions expected to work often failed whereas ionic adducts of the copolymer were clearly detected with some matrix/salt systems that were shown to badly perform for constituting homopolymers. Overall, this rules out the working assumption stating that the MALDI behavior of chains composed of PEO and PS segments should combine the behavior of the two polymeric species. Yet, although requiring a dedicated design of experiments, MALDI of the amphiphilic PEO-b-PS copolymer was achieved for the first time.

Cationization of neutral small molecules by site-specific carboxylation of 10-phenyl-10H-phenothiazine in laser desorption/ionization

It is a pre-requisite to ionize analyte molecules efficiently for detection by laser desorption/ionization mass spectrometry. Here, we report a conceptual demonstration of cationizing neutral small molecules which are typically difficult to be ionized with the traditional organic matrices due to their low proton/cation affinity values. Our strategy features generating radical cations from site-specifically carboxylated 10-(4-carboxyphenyl)-10H-phenothiazine-3,7-dicarboxylic acid (PTZ(A)₂-Ph(A)) with a laser, and anchoring the chlorine ion from NaCl through covalent bond-like bridging interactions with the N/S atoms in the heterocyclic structure. This "Maverick" design allows a dramatic change of the energy landscape of analyte sodiation with an enhanced efficiency. We have synthesized two families of compounds based on the model structures of phenothiazine (PTZ) and phenoxazine (PXZ) and their carboxylated derivatives, and performed comparison between them or against the traditional organic matrices in a systematic format. We have demonstrated that PTZ(A)₂-Ph(A) is outstanding as a novel MALDI matrix for the detection of oligosaccharides and amino acids, with an ultra-clean background baseline and high signal-to-noise ratios (up to dozens of times better than the traditional matrices). This work provides a new method for the cationization of neutral small molecules in a distinct mechanism, inspiring the development of next-generation matrices for sensitive detection of hard-to-be-ionized molecules by MALDI MS.

Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications

Background Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics. Content This review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories. Summary MALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases. Outlook There is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.

Lasers for matrix-assisted laser desorption ionization

Matrix-assisted laser desorption ionization (MALDI) was introduced 35 years ago and has advanced from a general method for producing intact ions from large biomolecules to wide use in applications ranging from bacteria identification to tissue imaging. MALDI was enabled by the development of high energy pulsed lasers that create ions from solid samples for analysis by mass spectrometry. The original lasers used for MALDI were ultraviolet fixed-wavelength nitrogen and Nd:YAG lasers, and a number of additional laser sources have been subsequently introduced with wavelengths ranging from the infrared to the ultraviolet and pulse widths from nanosecond to femtosecond. Wavelength tunable sources have been employed both in the IR and UV, and repetition rates have increased from tens of Hz to tens of kHz as MALDI has moved into mass spectrometry imaging. Dual-pulse configurations have been implemented with two lasers directed at the target or with a second laser creating ions in the plume of desorbed material. This review provides a brief history of the use of lasers for ionization in mass spectrometry and describes the various types of lasers and configurations used for MALDI.

Rapid Noninvasive Skin Monitoring by Surface Mass Recording and Data Learning

Skin problems are often overlooked due to a lack of robust and patient-friendly monitoring tools. Herein, we report a rapid, noninvasive, and high-throughput analytical chemical methodology, aiming at real-time monitoring of skin conditions and early detection of skin disorders. Within this methodology, adhesive sampling and laser desorption ionization mass spectrometry are coordinated to record skin surface molecular mass in minutes. Automated result interpretation is achieved by data learning, using similarity scoring and machine learning algorithms. Feasibility of the methodology has been demonstrated after testing a total of 117 healthy, benign-disordered, or malignant-disordered skins. Remarkably, skin malignancy, using melanoma as a proof of concept, was detected with 100% accuracy already at early stages when the lesions were submillimeter-sized, far beyond the detection limit of most existing noninvasive diagnosis tools. Moreover, the malignancy development over time has also been monitored successfully, showing the potential to predict skin disorder progression. Capable of detecting skin alterations at the molecular level in a nonsurgical and time-saving manner, this analytical chemistry platform is promising to build personalized skin care.

Investigations of the Equilibrium Conditions in Plumes of Laser Desorbed Sinapic Acid with Amino Acid Analytes: Influence of Sample Preparation and Matrix to Analyte Ratio

The equilibrium nature of a plume of laser desorbed material is examined through the application of a previously developed thermodynamic model to the ion signals observed in 337 nm MALDI mass spectra of mixtures of the matrix sinapic acid with the amino acids alanine, valine, isoleucine, and phenylalanine. Samples are prepared using both conventional dried-droplet and solvent-free methods for comparison. The relative yield of protonated amino acid is shown to increase as the amino acid gas-phase basicity increases for both sample preparation methods. Matrix gas phase basicity values extracted from the equilibrium plots are shown to be in good agreement ([M - H⁺]^• 876 kJ/mol and [M] 879 kJ/mol) with published experimental values supporting a mechanism wherein the protonated sinapic acid and/or the matrix radical cation act as the proton donor species. These experiments further reveal that there is a large difference in the extracted plume effective temperatures with the solvent-free method yielding lower effective temperatures as compared to the dried-droplet sample preparation, e.g., 552 K versus 1296 K, respectively, at M/A 1:1 (mole/mole). In addition, these experiments suggest that plume effective temperatures decrease as the relative amount of matrix deposited with the analyte increases, regardless of the sample preparation method. Cumulatively, these observations suggest that the crystalline solid allows more efficient transfer of the photoexcitation energy during the sample desorption step, as compared to the solvent-free sample, and/or collisional cooling is more effective for the plume of material desorbed from the solvent-free sample as compared to the conventional dried-droplet sample.

Sensitive detection of clenbuterol by hybrid iridium/silicon nanowire-enhanced laser desorption/ionization mass spectrometry

There is increasing demand for anti-doping drug monitoring in sports and food safety checks by developing sensitive and fast analytical methods. Here we report the development of hybrid Ir/SiNW as a new MALDI matrix for the detection of small molecules. This matrix is characterized by sufficient UV absorption, low-noise background, and high efficiency in ionization of small molecules. Sensitive detection of clenbuterol (LOD: 0.18 pmol) and a variety of other small molecules has been achieved using the Ir/SiNW matrix with a reproducible performance. Compared to the individual components separately, the matrix of hybrid Ir/SiNW synthesized via in situ growth can promote the MS signal intensity by up to 10 fold under identical experimental conditions. We provide a unique mechanism for the high performance of the hybrid Ir/SiNW matrix with the characteristic properties of hydrogen atom transfer and enhanced protonation at the interface of the hybrid nanostructures. Our approach of using a hybrid Ir/SiNW matrix enables detection of clenbuterol quantitatively in complicated biological samples and in vivo experiments, promising a useful tool for food security and anti-doping drug monitoring in sports.

The cationization of synthetic polymers in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: Investigations of the salt-to-analyte ratio

Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique that when used to analyze synthetic polymer analytes often requires the addition of a metal cationization agent (herein termed the "salt"). The choice of both the matrix and the cationization agent needs to be taken into account when considering the polymer under study; different polymers have shown different affinities toward different cationization agents, and their selectivity can change as the matrix changes. Salt-to-analyte ratio (S/A) plots are used in this work to investigate the effect of the quantity of cationization agent employed in the analysis of a poly (methylmethacrylate) (PMMA) analyte with different MALDI matrices. The point at which analyte signal stops increasing with the added cationization agent is termed the "cation saturation point," and it was found to occur around a S/A of 1. When the analyte signal after this point remains constant, it is termed an "ideal case." The "non-ideal case" occurs when the analyte signal decreases after the cation saturation point. The amount of matrix present (measured as the matrix-to-analyte molar ratio, M/A) and the use of different counterions for the salt are also found to affect the intensity of the analyte signal. In non-ideal cases, changes in the counterion or an increase in the M/A are found to increase the analyte signal, often converting an initially observed non-ideal case into an ideal case. Several experiments attempting to uncover the reason for observation of the non-ideal S/A behavior are also described.

Matrix-Free Laser Desorption Ionization Mass Spectrometry as an Efficient Tool for the Rapid Detection of Opiates in Crude Extracts of Papaver somniferum

Having a long history of traditional medicinal applications, Papaver somniferum is also known as a source of various pharmacologically highly active opiates. Consequently, their detection from plant extracts is an important analytical task and generally addressed by methods of GC-MS and LC-MS. However, opiates do also show structural similarities to matrix molecules used in matrix-assisted laser desorption ionization (LDI) and may therefore ionize upon simple laser irradiation. Following this analytical approach, the present work thoroughly evaluated the direct detection of opiates by matrix-free LDI in crude extracts of P. somniferum. The method facilitated the identification of 10 reported opiates by their molecular formulas without any chromatographic prepurification. Moreover, a principal component analysis based on LDI-MS data permitted the correct grouping of all extracts according to their inherent chemistry. Concluding experiments on serial dilutions of thebaine further evaluated potential quantitative applications of the method. Overall results highlight the promising potential of LDI-MS for the swift detection of opiates in complex mixtures.

Mass spectrometry imaging to detect lipid biomarkers and disease signatures in cancer

BACKGROUND

Current methods to identify, classify, and predict tumor behavior mostly rely on histology, immunohistochemistry, and molecular determinants. However, better predictive markers are required for tumor diagnosis and evaluation. Due, in part, to recent technological advancements, metabolomics and lipid biomarkers have become a promising area in cancer research. Therefore, there is a necessity for novel and complementary techniques to identify and visualize these molecular markers within tumors and surrounding tissue.

RECENT FINDINGS

Since its introduction, mass spectrometry imaging (MSI) has proven to be a powerful tool for mapping analytes in biological tissues. By adding the label-free specificity of mass spectrometry to the detailed spatial information of traditional histology, hundreds of lipids can be imaged simultaneously within a tumor. MSI provides highly detailed lipid maps for comparing intra-tumor, tumor margin, and healthy regions to identify biomarkers, patterns of disease, and potential therapeutic targets. In this manuscript, recent advancement in sample preparation and MSI technologies are discussed with special emphasis on cancer lipid research to identify tumor biomarkers.

CONCLUSION

MSI offers a unique approach for biomolecular characterization of tumor tissues and provides valuable complementary information to histology for lipid biomarker discovery and tumor classification in clinical and research cancer applications.

An Inexpensive, simple calibration method for MALDI TOF/TOF systems

The array of analytes that can be measured by MADLI MS has created an equally vast range of calibration mixtures. The inherent problem with this is that acquiring all of them at commercial rates can be prohibitively expensive. With this in mind, we have created a low-cost alternative to the most commonly used peptide calibrants. We were able to achieve an overall 78 ppm mass accuracy across a mass range of 900 to 2500 Da which was comparable to the mass accuracy achievable with commercial peptide mixes and hence has become a viable alternative.

Novel ionization processes for use in mass spectrometry: 'Squeezing' nonvolatile analyte ions from crystals and droplets

Together with my group and collaborators, I have been fortunate to have had a key role in the discovery of new ionization processes that we developed into new flexible, sensitive, rapid, reliable, and robust ionization technologies and methods for use in mass spectrometry (MS). Our current research is focused on how best to understand, improve, and use these novel ionization processes which convert volatile and nonvolatile compounds from solids or liquids into gas-phase ions for analysis by MS using e.g. mass-selected fragmentation and ion mobility spectrometry to provide reproducible, accurate, and improved mass and drift time resolution. In my view, the apex was the discovery of vacuum matrix-assisted ionization (vMAI) in 2012 on an intermediate pressure matrix-assisted laser desorption/ionization (MALDI) source without the use of a laser, high voltages, or any other added energy. Only exposure of the matrix:analyte to the sub-atmospheric pressure of the mass spectrometer was necessary to initiate ionization. These findings were initially rejected by three different scientific journals, with comments related to 'how can this work?', 'where do the charges come from?', and 'it is not analytically useful'. Meanwhile, we and others have demonstrated analytical utility without a complete understanding of the mechanism. In reality, MALDI and electrospray ionization are widely used in science and their mechanisms are still controversially discussed despite use and optimization of now 30 years. This Perspective covers the applications and mechanistic aspects of the novel ionization processes for use in MS that guided us in instrument developments, and provides our perspective on how they relate to traditional ionization processes.

High Throughput Complementary Analysis and Quantitation of Metabolites by MALDI- and Silicon Nanopost Array-Laser Desorption/Ionization-Mass Spectrometry

Silicon nanopost array (NAPA) structures have been shown to be effective substrates for laser desorption/ionization-mass spectrometry (LDI-MS) and have been used to analyze a variety of samples including peptides, metabolites, drugs, explosives, and intact cells, as well as to image lipids and metabolites in tissue sections. However, no direct comparison has yet been conducted between NAPA-MS and the most commonly used LDI-MS technique, matrix-assisted laser desorption/ionization (MALDI)-MS. In this work, we compare the utility of NAPA-MS to that of MALDI-MS using two common matrices for the analysis of metabolites in cellular extracts and human urine. Considerable complementarity of molecular coverage was observed between the two techniques. Of 178 total metabolites assigned from cellular extracts, 68 were uniquely detected by NAPA-MS and 62 were uniquely detected by MALDI-MS. NAPA-MS was found to provide enhanced coverage of low-molecular weight compounds such as amino acids, whereas MALDI afforded better detection of larger, labile compounds including nucleotides. In the case of urine, a sample largely devoid of higher-mass labile compounds, 88 compounds were uniquely detected by NAPA-MS and 13 by MALDI-MS. NAPA-MS also favored more extensive alkali metal cation adduction relative to MALDI-MS, with the [M + 2Na/K - H]⁺ species accounting for as much as 97% of the total metabolite ion signal in positive mode. The capability of NAPA-MS for targeted quantitation of endogenous metabolites in urine via addition of isotopically labeled standards was also examined. Both NAPA-MS and MALDI-MS provided quantitative results in good agreement with one another and the concentrations reported in the literature, as well as good sample-to-sample reproducibility (RSD < 10%).

Characterizing and alleviating ion suppression effects in atmospheric pressure matrix-assisted laser desorption/ionization

RATIONALE

As a powerful ambient ion source, atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) enables direct analysis at atmospheric pressure/temperature and minimal sample preparation. With the increasing usage of AP-MALDI sources with Orbitrap instruments, systematic characterization of the extent of ion suppression effect (ISE) in AP-MALDI-Orbitrap mass spectrometry imaging (MSI) is desirable. Recently, a new low-pressure MALDI platform has been introduced that reportedly provided better sensitivity. While extensive research efforts have been devoted to improving spatial resolution, fewer studies focused on the characterization and sensitivity improvement of these MALDI platforms that, coupled with high-resolution Orbitraps, provide powerful strategy for MSI.

METHODS

We compared the analytical performance of AP and low-pressure (subatmospheric) MALDI sources to study the effect of pressure control in the ion source. Using a model peptide/protein mixture, we systematically evaluated the factors influencing ISE. Furthermore, the effect of laser spot size was evaluated through tissue imaging analysis of lipids and neuropeptides. The effects of ion suppression and laser spot size have also been examined by comparing the number of identified molecular species during MSI analysis.

RESULTS

Several key operating parameters including source pressure, laser energy, laser repetition rate, and microscopic slide coating materials were optimized to minimize the ISE. Under the optimal conditions, the subatmospheric AP-MALDI-Orbitrap platform with high spatial and mass spectral resolution enabled significantly improved coverage of several lipid and neuropeptide families in the MS analysis of mouse brain tissue sections.

CONCLUSIONS

The new SubAP-MALDI source coupled with an Orbitrap mass spectrometer was established as a viable platform for in situ endogenous biomolecular analysis with increased sensitivity compared with conventional AP-MALDI sources as evidenced by the confident identification of neuropeptides from mouse brain imaging analyses. The alleviated ISE was key to substantial performance improvement due to optimized intermediate pressure conditions and better ion collection by the ion funnel.

Neutralization of insulin by photocleavage under high vacuum

Electrosprayed peptide ion beams are charge manipulated by photocleavage of chemical tags.

1,5-Diaminonaphtalene is a Highly Performing Electron-Transfer Secondary-Reaction Matrix for Laser Desorption Ionization Mass Spectrometry of Indolenine-Based Croconaines

Croconaine dyes are appealing molecules synthesized via the condensation of croconic acid and reactive electron-donating aromatic or heterocyclic systems. Here, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) investigation of indolenine-based croconaines is presented for the first time. Archetype proton-transfer matrices, such as 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA), 9-aminoacridine (9AA) as the protonating/deprotonating matrix, and electron-transfer (ET) secondary-reaction matrices, such as 1,5-diaminonapthalene (DAN) and trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), were investigated. DHB, CHCA, and 9AA generate a mix of odd-electron molecular ions and protonated, sodiated, and potassiated adducts. Among the ET matrices, DAN was found to be capable of directing the ionization process toward the exclusive formation of odd-electron molecular ions M^+• without fragmentation. MALDI tandem MS provides useful structural characterization of croconaine dyes, thus making identification very straightforward for all investigated compounds. Interestingly the fragmentation of bromo-containing croconaines revealed, for the first time, the gas-phase formation of a bromime cation [Br]⁺.