Gas-phase basicities of the isomeric dihydroxybenzoic acids and gas-phase acidities of their radical cations

The thermochemical acid/base properties of the six dihydroxybenzoic acids (x,y-DHB) as prototypical matrices used in matrix-assisted laser desorption/ionization (MALDI) have been investigated. The ground-state gas-phase basicities (GB) of the six DHB isomers and the gas-phase acidities (deltaG acid) of the corresponding radical cations ([x,y-DHB]*+) have been determined by Fourier-transform ion cyclotron resonance mass spectrometry employing the thermokinetic method. The gas-phase basicities vary from 814 kJ mol-1 for the least basic isomer, 3,5-DHB, to 831 kJ mol-1 for the most basic isomer, 2,4-DHB. The obtained gas-phase acidities of the corresponding radical cations vary from 815 kJ mol-1 for the most acidic species, 3,4-DHB, to 858 kJ mol-1 for the least acidic one, 2,5-DHB. The results indicate that ground-state proton transfer from the matrix radical cations to the analyte may play a role in the ionization process of MALDI, whereas proton transfer from protonated matrix molecules can be excluded.     

Effect of matrix crystal structure on ion abundance of carbohydrates by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry

Sample preparation techniques for carbohydrate analysis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are explored, with particular emphasis on analyte/matrix co-crystallization procedures. While carbohydrates are known to prefer 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix of choice, these analytes are quite specific about matrix crystal structure, which in turn is dependent on the rate of drying of analyte/matrix spots on the MALDI target. With N-acetylglucosamine (GlcNAc) and N-acetylneuraminic acid (sialic acid or NeuAc) as test monosaccharides, significant increases in ion abundances are demonstrated with 2,5-DHB/NeuAc spots (>10-fold improvement) and 2,5-DHB/GlcNAc spots ( approximately 5-fold improvement) with active drying. The fine structure of crystals generated in active and passive drying was investigated using powder diffraction. Passively dried samples were shown to consist of an ordered polymorph, crystallizing in the space group P2(1)/a, while the actively dried samples produced a disordered phase crystallizing in the space group Pa. These data provide the wherewithal to engineer a matrix best suited for carbohydrate analyses.     

Measuring salty samples without adducts with MALDI MS

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been used for the discovery of hundreds of novel cell to cell signaling peptides. Beyond its advantages of sensitivity and minimal sample preparation requirements, MALDI MS is attractive for biological analyses as high quality mass spectra may be obtained directly from specific locations within prepared tissue sections. However, due to the large quantity of salts present in physiological tissues, these mass spectra often contain many adducts of cationic salts such as sodium and potassium, in addition to the molecular ion [M + H]⁺. To reduce the presence of cation adducts in MALDI mass spectra obtained directly from tissues, we present a methodology that uses a slow condensation procedure to enable the formation of distinct regions of matrix/analyte crystals and cation (salt) crystals. Secondary ion mass spectrometric imaging suggests that the salts and MALDI matrix undergo a mutually exclusive crystallization process that results in the separation of the salts and matrix in the sample.     

Computational study of matrix-peptide interactions in MALDI mass spectrometry: Interactions of 2,5- and 3,5-dihydroxybenzoic acid with the tripeptide valine-proline-leucine

The mechanism of matrix-to-analyte proton transfer in matrix-assisted laser desorption and ionization mass spectrometry (MALDI-MS) has been investigated computationally by modeling the matrix-analyte interaction of potential MALDI matrixes such as 2,5-dihydroxybenzoic acid (2,5-DHB) and 3,5-DHB with the tripeptide valine-proline-leucine (VPL). A combination of molecular dynamics/simulated annealing calculations followed by density functional theory geometry optimization using a reasonably large basis set has been done on a large number of clusters in an attempt to study the ionization energy of each matrix in the cluster environment and the intracluster proton transfer from the matrix to the tripeptide. The calculations show a substantial reduction in the IP for both matrixes in their cluster environments. In the 2,5-system, proton transfer can sometimes occur in the neutral clusters (preformed ions), whereas proton transfer in the cationic clusters, which is actually a double proton transfer, is spontaneous and exoergic. Even though it is more acidic from a thermodynamic perspective, the radical cation of 3,5-DHB is a less efficient proton donor to VPL. The thermodynamics of proton transfer in the cationic clusters is discussed in detail.     

Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to rapidly screen for albuminuria

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is used as an alternative method for the rapid diagnosis of albuminuria. This technique requires no further sample pretreatment than simply mixing the urine sample with a MALDI matrix and drying under ambient conditions. The resulting MALDI mass spectra reveal albumin ions having charges ranging from +1 to +5. The detection of albumin is possible using any of the three most common MALDI matrices - sinapinic acid (SA), 2,5-dihydroxybenzoic acid (2,5-DHB), or 4-hydroxy-alpha-cyanocinnamic acid (alpha-CHC). Using this analytical approach, the limit of detection for albumin in urine is 10(-6) M, approximately 5 to 10 times lower than that detectable through conventional chemical testing.     

Glass-chip-based sample preparation and on-chip trypic digestion for matrix-assisted laser desorption/ionization mass spectrometric analysis using a sol-gel/2,5-dihydroxybenzoic acid hybrid matrix

A glass-chip-based sample preparation method for matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis of tryptic digests of proteins and intact cells is described. A MALDI matrix, 2,5-dihydroxybenzoic acid (2,5-DHB), was hybridized with sol-gels to generate a sol-gel-derived material. Taking advantage of the characteristics of sol-gels, the sol-gel-derived material readily adhered to the surface of a glass chip through covalent bonding. Only one step of sample preparation, deposition of the sample solution on the glass chip, was required before MALDI-MS analysis. Because 2,5-DHB was homogeneously dispersed on the sol-gel network structure, good spot-to-spot reproducibility was obtained in MALDI analysis using this approach and the analyte signals were uniform throughout the chip. The modified glass chips were robust and effective for at least 1 week. This glass-chip-based matrix preparation method provides a straightforward approach to developing techniques for analyzing the on-chip enzymatic digestion of proteins and intact cells of microorganisms. Cytochrome C and Escherichia coli were used as analytes to demonstrate the feasibility of this approach. The products of the on-chip enzymatic digests were identified through protein database searches.     

Solvent selection for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric analysis of synthetic polymers employing solubility parameters

The principle relating to the selection of a proper matrix, cationization reagent, and solvent for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) of synthetic polymers is still a topic of research. In this work we focused on the selection of a suitable MALDI solvent. Polystyrene PS7600 and poly(ethylene glycol) PEG4820 were analyzed by MALDI‐TOF MS using various solvents which were selected based on the Hansen solubility parameter system. For polystyrene (PS), dithranol was used as the matrix and silver trifluoroacetate as the cationization reagent whereas, for poly(ethylene glycol) (PEG), the combination of 2,5‐dihydroxybenzoic acid and sodium trifluoroacetate was used for all experiments. When employing solvents which dissolve PS and PEG, reliable MALDI mass spectra were obtained while samples in non‐solvents (solvents which are not able to dissolve the polymer) failed to provide spectra. It seems that the solubility of the matrix and the cationization reagent are less important than the polymer solubility. Copyright © 2010 John Wiley & Sons, Ltd.     

Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues

The changes in the ion signals in the isotope cluster, mass resolution, signal-to-noise ratio and mass accuracy for matrix-assisted laser desorption/ionization (MALDI) of DNA oligonucleotides (dGGATC, dCAGCt, and dAACCGTT) and their fragment ions were evaluated, and these data were compared with those obtained using 3-hydroxypicolinic acid. Mass spectra obtained by using 2,5-dihydroxybenzoic acid (2,5-DHB) appear to have differences from the theoretical isotopic clusters, which arise by reductive hydrogenation producing a second peak at the M + 2 isotope of the native oligonucleotide. Based on the patterns of the isotopic envelope observed in the in-source decay fragments, we propose that cytosine is the site of reduction. We do not find evidence of reduction of oligonucleotides, viz. dTGGGGTT, that do not contain cytosine; however, 2'-deoxycytidine and 2'-deoxycytidine-5'-monophosphate undergo reductive hydrogenation. Several experiments were carried out in an effort to determine whether the reductive hydrogenation occurs during sample preparation or as a result of laser irradiation. The results of these experiments suggest that it occurs during sample preparation. The relative intensities of ion signals corresponding to the reduced base can be altered by using different matrix additives (aminonaphthalenes) or a different substrate (copper). Also, the oxidized form of 2,5-DHB is trapped by reaction with the side chain of cysteine in glutathione, providing evidence that the reaction occurs in solution as the matrix crystallizes.     

Examination of complex oligosaccharides by matrix-assisted laser desorption/ionization mass spectrometry on time-of-flight and magnetic sector instruments

Matrix-assisted laser desorption/ionization (MALDI) spectra of underivatized oligosaccharides of the type attached to asparagine in glycoproteins (N-linked oligosaccharides) were examined with linear time-of-flight (TOF) and magnetic sector instruments using 2,5-dihydroxybenzoic acid (2,5-DHB), α-cyano-4-hydroxycinnamic acid, sinapinic acid, 1,4-dihydroxynaphthalene-2-carboxylic acid or 2-(4-hydroxyphenylazo)benzoic acid (HABA) as the matrices. All compounds formed abundant [M + Na]⁺ ions with the strongest signals being obtained from 2,5-DHB after recrystallization of the initially dried sample spot from ethanol. Only traces of fragmentation were detected from neutral oligosaccharides on the TOF system but more abundant fragment ions (about 5% relative abundance) were present in the spectra from the magnetic sector instrument. Fragmentation was dominated by Y-type glycosidic cleavages (Domon and Costello nomenclature) between all sugar residues yielding sequence and branching information. Sialic acid-containing oligosaccharides generally produced the sodium adduct of the sodium salt and gave much weaker signals than the neutral sugars in the positive-ion mode. There was also considerable loss of the sialic acid moleties as the result of fragmentation on the magnetic sector instrument. The least fragmentation of both neutral and acidic sugars was caused by 2.5 DHB, which proved to be the most appropriate matrix for examination of oligosaccharide mixtures. Much better resolution of the oligosaccharides was obtained than by traditional methods such as the use of Bio-Gel P-4 gel filtration column chromatography. It is worth noting also that the measurements were considerably faster (a few minutes as opposed to about 16 h). In addition, no radiolabelling was necessary as required for detection on the P-4 columns. Mixtures of oligosaccharides from several glycoproteins (ribonuclease B, human immunoglobulin G (IgG) transferrin, bovine fetuin and chicken ovalbumin) were examined and the patterns of the identified oligosaccharides were found to agree closely with the known compositions of the sugar mixtures. The mass spectrometric resolution on the magnetic sector instrument was very much better (up to 3000, FWHM) than could be obtained with the linear TOF systems (200–400). The technique was used as a detection system for the products of exoglycosidase digestion in experiments to determine the detailed structure of the oligosaccharide chains from human IgG.     

Artifact-free matrix-assisted laser desorption ionization time-of-flight mass spectra of tert.-butyldimethylsilyl ether derivatives of cyclodextrins used for the synthesis of single-isomer, chiral resolving agents for capillary electrophoresis

Artifact-free, high-resolution matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectra have been obtained for the labile, single-isomer, tert.-butyldimethylsilyl ether derivatives of alpha-, beta- and gamma-cyclodextrins by optimizing the MALDI sample preparation method. 2,5-Dihydroxybenzoic acid, a 3:1 mixture of 2,5-dihydroxybenzoic acid and 1-hydroxyisoquinoline, and 2,4,6-trihydroxyacetophenone were investigated as MALDI matrices with methanol and acetonitrile as matrix solvents. Partial-to-complete loss of the tert.-butyldimethylsilyl groups was observed when the commonly used 2,5-dihydroxybenzoic acid was the MALDI matrix and/or methanol was the solvent, both with and without trifluoroacetic acid as additive. Loss of the labile tert.-butyldimethylsilyl groups was avoided with 2,4,6-trihydroxyacetophenone as MALDI matrix and acetonitrile as matrix solvent. Good ion intensities were achieved for the (M+Na)+ and (M+K)+ quasimolecular ions in the positive-ion mode. Minor byproducts were observed in some of the samples and the information was used to aid the optimization of the synthetic work.     

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.     

Improved MALDI-TOF Microbial Mass Spectrometry Imaging by Application of a Dispersed Solid Matrix

The key step in high quality microbial matrix-assisted laser desorption/ionization mass spectrometry imaging (microbial MALDI MSI) is the fabrication of a homogeneous matrix coating showing a fine-grained morphology. This application note addresses a novel method to apply solid MALDI matrices onto microbial cultures grown on thin agar media. A suspension of a mixture of 2,5-DHB and α-CHCA is sprayed onto the agar sample surface to form highly homogeneous matrix coatings. As a result, the signal intensities of metabolites secreted by the fungus Aspergillus fumigatus were found to be clearly enhanced.

Phosphoric acid enhances the performance of Fe(III) affinity chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for recovery, detection and sequencing of phosphopeptides

An integrated analytical strategy for enrichment, detection and sequencing of phosphorylated peptides by matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) is reported. o-Phosphoric acid was found to enhance phosphopeptide ion signals in MALDI-MS when used as the acid dopant in 2,5-dihydroxybenzoic acid (2,5-DHB) matrix. The effect was largest for multiply phosphorylated peptides, which exhibited an up to ten-fold increase in ion intensity as compared with standard sample preparation methods. The enhanced phosphopeptide response was observed during MALDI-MS analysis of several peptide mixtures derived by proteolytic digestion of phosphoproteins. Furthermore, the mixture of 2,5-DHB and o-phosphoric acid was an excellent eluant for immobilized metal affinity chromatography (IMAC). Singly and multiply phosphorylated peptide species were efficiently recovered from Fe(III)-IMAC columns, reducing sample handling for phosphopeptide mapping by MALDI-MS and subsequent phosphopeptide sequencing by MALDI-MS/MS. The enhanced response of phosphopeptide ions in MALDI facilitates MS/MS of large (>3 kDa) multiply phosphorylated peptide species and reduces the amount of analyte needed for complete characterization of phosphoproteins.     

Quantitative reproducibility of mass spectra in matrix‐assisted laser desorption ionization and unraveling of the mechanism for gas‐phase peptide ion formation

In a previous study on matrix‐assisted laser desorption ionization (MALDI) of peptides using α‐cyano‐4‐hydroxycinnamic acid (CHCA) as a matrix, we found that the patterns of single‐shot spectra obtained under different experimental conditions became similar upon temperature selection. In this paper, we report that absolute ion abundances are also similar in temperature‐selected MALDI spectra, even when laser fluence is varied. The result that has been obtained using CHCA and 2,5‐dihydroxybenzoic acid as matrices is in disagreement with the hypothesis of laser‐induced ionization of matrix as the mechanism for primary ion formation in MALDI. We also report that the total number of ions in such a spectrum is unaffected by the identity, concentration and number of analytes, i.e. it is the same as that in the spectrum of pure matrix. We propose that the generation of gas‐phase ions in MALDI can be explained in terms of two thermal reactions, i.e. the autoprotolysis of matrix molecules and the matrix‐to‐analyte proton transfer, both of which are in quasi‐equilibrium in the early matrix plume. Copyright © 2013 John Wiley & Sons, Ltd.     

In-source decay and fragmentation characteristics of peptides using 5-aminosalicylic acid as a matrix in matrix-assisted laser desorption/ionization mass spectrometry

The use of 5-aminosalicylic acid (5-ASA) as a new matrix for in-source decay (ISD) of peptides including mono- and di-phosphorylated peptides in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is described. The use of 5-ASA in MALDI-ISD has been evaluated from several standpoints: hydrogen-donating ability, the outstanding sharpness of molecular and fragment ion peaks, and the presence of interference peaks such as metastable peaks and multiply charged ions. The hydrogen-donating ability of several matrices such as α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), 1,5-diaminonaphthalene (1,5-DAN), sinapinic acid (SA), and 5-ASA was evaluated by using the peak abundance of a reduction product [M + 2H + H]⁺ to that of non-reduced protonated molecule [M + H]⁺ of the cyclic peptide vasopressin which contains a disulfide bond (S-S). The order of hydrogendonating ability was 1,5-DAN > 5-ASA > 2,5-DHB > SA = CHCA. The chemicals 1,5-DAN and 5-ASA in particular can be classified as reductive matrices. 5-ASA gave peaks with higher sharpness for protonated molecules and fragment ions than other matrices and did not give any interference peaks such as multiply-protonated ions and metastable ions in the ISD mass spectra of the peptides used. Particularly, 1,5-DAN and 5-ASA gave very little metastable peaks. This indicates that 1,5-DAN and 5-ASA are more “cool” than other matrices. The 1,5-DAN and 5-ASA can therefore be termed “reductive cool” matrix. Further, it was confirmed that ISD phenomena such as N-Cα bond cleavage and reduction of S-S bond is a single event in the ion source. The characteristic fragmentations, which form a− and (a + 2)-series ions, [M + H − 15]⁺, [M + H − 28]⁺, and [M + H − 44]⁺ ions in the MALDI-ISD are described.     

Azo-group reduction during the matrix-assisted laser desorption/ionization process in the presence of 2,5-dihydroxybenzoic acid

Some time ago, we published an announcement that the azo group that closes model cyclic peptides is often reduced in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) in the presence of 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix. In this work, we demonstrate that these peptides are ionized in all DHB matrix isomers, although threshold ionization laser energies as well as the reduction ratios differ in each matrix. Using a NALDI plate, we confirmed that their reduction depends on the presence of DHB matrix and that the hydrogen atoms participating in the reaction come from the DHB matrix hydroxyl group. We show that the reduction ratio is affected by the overall covalent structure of the peptide, by the presence of a free carboxyl group in DHB matrix, by the mutual position of the hydroxyl and carboxyl groups, as well as the laser beam intensity. Based on these results, it can be concluded that the azo-group reduction in cyclic peptides is a very complex process and we are far from fully understanding its nature. We hope that our experimental results will help to shed some light on the MALDI process that still remains mysterious in some of its aspects.     

Comparison of ionization behaviors of ring and linear carbohydrates in MALDI-TOFMS

Ionization efficiencies of cyclodextrins and their linear compounds in matrix-assisted laser desorption and ionisation (MALDI) analysis were compared, and differences in the ionization efficiencies of α- and β-cyclodextrins were also studied. The mass spectra showed a series of the [M+cation]⁺ ions but not the [M+H]⁺ ions. Alkali metal salts of Li⁺, Na⁺, K⁺, and Cs⁺ were used as the cationizing agents to enhance the ionization efficiency. Relative ion intensities of the ring compounds (α- and β-cyclodextrins) were much larger than those of the linear ones (maltohexaose and maltoheptaose), and the difference showed an increasing trend with the size of the alkali metal cation. β-Cyclodextrin had higher ionization efficiency than α-cyclodextrin and the difference increased by increasing the size of the alkali metal cation. It was also found that the ionization efficiency was affected by the counter anion of the salt. The higher ionization efficiencies of cyclodextrins were explained with the number of coordination sites and the binding energies.     

Method development for the analysis of resinous materials with MALDI‐FT‐ICR‐MS: novel internal standards and a new matrix material for negative ion mode

Matrix‐assisted laser desorption/ionization (MALDI) is a mass spectrometry (MS) ionization technique suitable for a wide variety of sample types including highly complex ones such as natural resinous materials. Coupled with Fourier transform ion cyclotron resonance (FT‐ICR) mass analyser, which provides mass spectra with high resolution and accuracy, the method gives a wealth of information about the composition of the sample. One of the key aspects in MALDI‐MS is the right choice of matrix compound. We have previously demonstrated that 2,5‐dihydroxybenzoic acid is suitable for the positive ion mode analysis of resinous samples. However, 2,5‐dihydroxybenzoic acid was found to be unsuitable for the analysis of these samples in the negative ion mode. The second problem addressed was the limited choice of calibration standards offering a flexible selection of m/z values under m/z 1000. This study presents a modified MALDI‐FT‐ICR‐MS method for the analysis of resinous materials, which incorporates a novel matrix compound, 2‐aminoacridine for the negative ion mode analysis and extends the selection of internal standards with m/z <1000 for both positive (15 different phosphazenium cations) and negative (anions of four fluorine‐rich sulpho‐compounds) ion mode. The novel internal calibration compounds and matrix material were tested for the analysis of various natural resins and real‐life varnish samples taken from cultural heritage objects. Copyright © 2017 John Wiley & Sons, Ltd.     

Analysis of hydrocarbon polymers by matrix-assisted laser desorption / ionization-fourier transform mass spectrometry

A quick and effective sample preparation is demonstrated for matrix-assisted laser desorption/ionization (MALDI) analysis of nonpolar polymers. Polyisoprene, polystyrene, and polybutadiene polymers were investigated by using as matrix a 2,5-dihydroxybenzoic acid and silver nitrate combination. Silver cationized oligomers produce useful spectra that can be signal averaged to characterize polymer distributions extending up to 6000 u by using a 3-T Fourier transform mass spectrometer. Because an electrostatic ion deceleration protocol was used to extend the mass range, trapping discrimination is shown to exist for molecular weight distributions broader than about 2500 u. However, an integral procedure can be used to reconstruct the true polymer profiles through co-addition of signal transients obtained by using various gated deceleration times. For polymers with narrower mass distributions, silver cationization along with signal averaging provides rapid and accurate polymer characterization for nonpolar polymer systems by using standard MALDI Fourier transform mass spectrometry instrumentation.     

Negative ion production from peptides and proteins by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Negative ion production from peptides and proteins was investigated by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry. Although most research on peptide and protein identification with ionization by MALDI has involved the detection of positive ions, for some acidic peptides protonated molecules are not easily formed because the side chains of acidic residues are more likely to lose a proton and form a deprotonated species. After investigating more than 30 peptides and proteins in both positive and negative ion modes, [M–H]⁻ ions were detected in the negative ion mode for all peptides and proteins although the matrix used was 2,5‐dihydroxybenzoic acid (DHB), which is a good proton donor and favors the positive ion mode production of [M+H]⁺ ions. Even for highly basic peptides without an acidic site, such as myosin kinase inhibiting peptide and substance P, good negative ion signals were observed. Conversely, gastrin I (1‐14), a peptide without a highly basic site, will form positive ions. In addition, spectra obtained in the negative ion mode are usually cleaner due to absence of alkali metal adducts. This can be useful during precursor ion isolation for MS/MS studies. Copyright © 2008 John Wiley & Sons, Ltd.