Identification of dinucleoside polyphosphates by matrix-assisted laser desorption/ionisation post-source decay mass spectrometry

Dinucleoside polyphosphates are a group of intra- and extracellular mediators controlling numerous physiological functions. In this study dinucleoside polyphosphates were examined by positive ion matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MADLI-TOFMS). 3-Hydroxypicolinic acid was used as UV-absorbing matrix. For the individual dinucleoside polyphosphates Ap(n)A (n = 2-7), Ap(n)G (n = 2-6) and Gp(n)G (n = 2-6), MALDI post-source decay (PSD) mass spectra were measured. Each mass peak in the MALDI-PSD mass spectra could be assigned to individual fragments of dinucleoside polyphosphates. The comparison of the fragmentation patterns of the dinucleoside polyphosphates presented here demonstrates that dinucleoside polyphosphates preferably cleave to fragment ions consisting of the corresponding mononucleoside polyphosphates as well as the corresponding nucleosides and bases during flight in the field-free drift path of the MALDI mass spectrometer. Therefore, the MALDI-PSD approach described here is suitable for identification of other dinucleoside polyphosphates. The present MALDI-PSD mass spectra may be used as MALDI-PSD mass reference spectra for future identification of dinucleoside polyphosphates and other nucleotides.     

Quantitative estimation of geometric isomers by post-source decay MALDI MS

Isomeric triazine pesticides: prometryn (N,N′-bis(1-methylethyl)-6-(methylthio)-1,3,5-triazine-2,4-diamine) and terbutryn (N-(1,1-dimethylethyl)-N′-ethyl-6-(methylthio)-1,3,5-triazine-2,4-diamine) are quantitatively analyzed by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) without prior separation. The total concentration of the pesticide isomers was quantified by ‘standard’ MALDI using simetryn as an internal standard, while the composition of the isomeric mixture was estimated using post-source decay (PSD) MALDI-MS. Prometryn and terbutryn generate different PSD-MALDI product ions, and a PSD fragment characteristic of each isomeric pesticide is used for quantification of the mixture. Specifically, the fragment at m/z=186 is used for quantification of terbutryn, while the fragment at m/z=200 is used for prometryn. Fast evaporation and dried droplet methods were employed in PSD-MALDI quantification, and linear signal response was obtained for both methods. However, the fast evaporation method showed better quantitative characteristics and a lower detection limit.     

Identification of GlcNAcylation sites of peptides and alpha-crystallin using Q-TOF mass spectrometry

The addition of a single N-acetylglucosamine residue O-linked to serine and threonine residues of nuclear and cytoplasmic proteins is a widespread modification throughout all eukaryotes. The conventional method for detecting and locating sites of modification is a multi-step radioactivity-based protocol. In this paper we show that using quadrupole time-of-flight (Q-TOF) mass spectrometry, modification sites can be identified at a significantly higher sensitivity than previous approaches. This is the first demonstration that sites of O-GlcNAcylation can be identified directly using mass spectrometry.     

Identification and fragmentation study of plasticizers with post-source decay matrix-assisted laser desorption/ionization mass spectrometry

A detailed investigation of the most commonly used plasticizers, such as phthalate, adipate and trimellitate esters, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and post-source decay (PSD) MALDI-TOFMS/MS is described. It is shown that PSD MALDI-TOFMS/MS is capable of unambiguous determination of the different types of plasticizers. The determination of the types of plasticizers from different PVC samples by PSD MALDI-TOFMS/MS, without the need for solvent extraction, is also demonstrated. The fragmentation mechanisms of these plasticizers cationized with protons and sodium ions are also reported.     

Structural analysis of secondary ions by post-source decay in time-of-flight secondary ion mass spectrometry

Tandem mass spectrometry measurements have been achieved using time-of-flight secondary ion mass spectrometry (TOF-SIMS) and a post source decay (PSD)-like method. The performance of the method has been demonstrated on model molecules with well-known fragmentation pathways. Several lipids have been fragmented including the phosphocholine ion, phosphatidylcholines, cholesterol and vitamin E. Pure samples were analyzed, and the results compared with those obtained with the same compounds on a quadrupole-TOF hybrid mass spectrometer. Then, the structures of some lipids which are currently observed in the TOF-SIMS imaging of mammalian tissue sections were verified.     

Identification of selenomethionine in selenized yeast using two-dimensional liquid chromatography-mass spectrometry based proteomic analysis

Selenium-enriched yeast has been commonly used as a nutritional supplement. Here we describe a protocol used to investigate the metabolic fate of inorganic selenium in yeast. We provide definitive, mass spectrometry based evidence for the non-specific incorporation of selenomethionine in the yeast proteome involving the replacement of about 30% of all methionine with selenomethionine.     

Structure analysis of branched oligosaccharides using post-source decay in matrix-assisted laser desorption ionization mass spectrometry

Post-source decay matrix-assisted laser desorption ionization (PSD-MALDI) of sodium ion-attached branched oligosaccharides derived from glycoproteins was demonstrated as a method of structure analysis by reflectron time-of-flight (TOF) mass spectrometry. Mono-, di- and triantennary structures were investigated. The fragmentation patterns of these (structurally related) substances as obtained in the positive-ion mode showed characteristic differences correlated with branching sites and linkage positions. Two-bond ring cleavages as known from fast atom bombardment/collision-induced dissociation and IR laser desorption mass spectrometry were also observed. Internal fragment ions formed by up to four consecutive cleavages were obtained with high intensity, allowing the branching structure of complex carbohydrates to be identified. PSD-MALDI of oligosaccharides is characterized by high sensitivity, very good signal-to-noise ratios and high reproducibility of fragmentation patterns and signal intensities.     

Rapid detection of apoptosis in mammalian cells by using intact cell MALDI mass spectrometry

Detection of cell death has extensive applications and is of great commercial value. However, most current high-throughput cell viability assays cannot distinguish the two major forms of cell death: apoptosis and necrosis. Many apoptosis-specific detection methods exist but they are time consuming and labour intensive. In this work, we proposed a novel approach based on Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) for the specific detection of apoptosis in cultured mammalian cells. Buffer washed cells were directly mixed with a matrix solution and subsequently deposited onto the stainless steel target for MALDI analysis. The resulting mass spectrometric profiles were highly reproducible and can be used to reflect cell viability. Remarkably, the mass spectrometric profiles generated from apoptotic cells were distinct from those from either normal or necrotic cells. The apoptosis-specific features of the mass spectra were proportional to the percentage of apoptotic cells in the culture, but are independent of the drugs used to stimulate apoptosis. This is the first report on the utilization of intact cell MALDI mass spectrometry in detecting mammalian cell apoptosis, and can be used as a basis for the development of a reliable, fast, label-free and high-throughput method for detecting apoptotic cell death.     

Structural analysis of phosphatidylcholines by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The utility of post-source decay (PSD) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was investigated for the structural analysis of phosphatidylcholine (PC). PC did not produce detectable negative molecular ion from MALDI, but positive ions were observed as both [PC+H](+) and [PC+Na](+). The PSD spectra of the protonated PC species contained only one fragment corresponding to the head group (m/z 184), while the sodiated precursors produced many fragment ions, including those derived from the loss of fatty acids. The loss of fatty acid from the C-1 position (sn-1) of the glycerol backbone was favored over the loss of fatty acid from the C-2 position (sn-2). Ions emanating from the fragmentation of the head group (phosphocholine) included [PC+Na-59](+), [PC+Na-183](+) and [PC+Na-205](+), which corresponded to the loss of trimethylamine (TMA), non-sodiated choline phosphate and sodiated choline phosphate, respectively. Other fragments reflecting the structure of the head group were observed at m/z 183, 146 and 86. The difference in the fragmentation patterns for the PSD of [PC+Na](+) compared to [PC+H](+) is attributed to difference in the binding of Na(+) and H(+). While the proton binds to a negatively charged oxygen of the phosphate group, the sodium ion can be associated with several regions of the PC molecule. Hence, in the sodiated PC, intermolecular interaction of the negatively charged oxygen of the phosphate group, along with sodium association at multiple sites, can lead to a complex and characteristic ion fragmentation pattern. The preferential loss of sn-1 fatty acid group could be explained by the formation of an energetically favorable six-member ring intermediate, as apposed to the five-member ring intermediate formed prior to the loss of sn-2 fatty acid group.     

Identification of by-products from an orthogonal peptide ligation by oxime bonds using mass spectrometry and tandem mass spectrometry

Synthetic proteins with unusual architecture are obtained through chemoselective ligation, a method based on the condensation of unprotected peptides under mild aqueous conditions. The last step of a new procedure leading to a tri-branched conjugate consists of the chemoselective ligation reaction between an (aminooxy)acetyl peptide and a peptide aldehyde resulting from a first ligation via an oxime bond. In order to optimize the reaction conditions, electrospray ionization mass spectrometry combined with liquid chromatography and tandem mass spectrometry has been used. In addition to the target tri-branched conjugate, two other conjugates were characterized allowing documentation of transoximation reactions in peptide chemistry. A fourth conjugate was identified as a side product appearing after the first ligation. Data obtained by low-energy collision-induced dissociation led to a rapid and reliable identification of impurities observed in the (aminooxy)acetyl peptide despite a previous high performance liquid chromatography (HPLC) purification. This highlights the great reactivity of the aminooxy group towards carbonyl-containing compounds.     

Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) mass spectrometry and its implications for protein identification

A study has been undertaken to evaluate the usefulness of MALDI Q-TOF data for protein identification. The comparison of MS data of protein digests obtained on a conventional MALDI TOF instrument to the MS data from the MALDI Q-TOF reveal peptide patterns with similar intensity ratios. However, comparison of MS/MS Q-TOF data produced by nanoelectrospray versus MALDI reveals striking differences. Peptide fragment ions obtained from doubly charged precursors produced by nanoelectrospray are mainly y-type ions with some b-ions in the lower mass range. In contrast, peptide fragment ions produced from the singly charged ions originating from the MALDI source are a mixture of y-, b- and a-ions accompanied by ions resulting from neutral loss of ammonia or water. The ratio and intensity of these fragment ions is found to be strongly sequence dependent for MALDI generated ions. The singly charged peptides generated by MALDI show a preferential cleavage of the C-terminal bond of acidic residues aspartic and glutamic acid and the N-terminal bond of proline. This preferential cleavage can be explained by the mobile proton model and is present in peptides that contain both arginine and an acidic amino acid. The MALDI Q-TOF MS/MS data of 24 out of 26 proteolytic peptides produced by trypsin or Asp-N digestions were successfully used for protein identification via database searching, thus indicating the general usefulness of the data for protein identification. De novo sequencing using a mixture of 160/18O water during digestion has been explored and de novo sequences for a number of peptides have been obtained.     

Fragmentation and sequencing of cyclic peptides by matrix-assisted laser desorption/ionization post-source decay mass spectrometry.

A series of synthetic cyclic decapeptides and other smaller cyclic peptides were analyzed using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The investigated compounds were cyclized in a head-to-tail manner and contained non-proteinaceous amino acids, such as D-phenylalanine, D,L-4-carboxyphenylalanine, epsilon-aminocaproic acid, and gamma-aminobutyric acid, and were synthesized in a program to develop inhibitors of pp60(c-src) (Src), a tyrosine kinase that is involved in signal transduction and growth regulation. Post-source decay (PSD) spectra of the cyclic peptides featured abundant sequence ions. Two preferential ring opening reactions were detected resulting in linear fragment ions with an N-terminus of proline and a C-terminus of glutamic acid, respectively. MALDI-PSD spectra even permitted de novo sequencing of some cyclic peptides. Systematic studies on cyclic peptides using this method of fragmentation have not been reported to date. This work presents an easy mass spectrometric method, MALDI-PSD, for the characterization and identification of cyclic peptides.     

Identification of oligosaccharides from histopathological sections by MALDI imaging mass spectrometry

Direct tissue analysis using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) provides the means for in situ molecular analysis of a wide variety of biomolecules. This technology—known as imaging mass spectrometry (IMS)—allows the measurement of biomolecules in their native biological environments without the need for target-specific reagents such as antibodies. In this study, we applied the IMS technique to formalin-fixed paraffin-embedded samples to identify a substance(s) responsible for the intestinal obstruction caused by an unidentified foreign body. In advance of IMS analysis, some pretreatments were applied. After the deparaffinization of sections, samples were subjected to enzyme digestion. The sections co-crystallized with matrix were desorbed and ionized by a laser pulse with scanning. A combination of α-amylase digestion and the 2,5-dihydroxybenzoic acid matrix gave the best mass spectrum. With the IMS Convolution software which we developed, we could automatically extract meaningful signals from the IMS datasets. The representative peak values were m/z 1,013, 1,175, 1,337, 1,499, 1,661, 1,823, and 1,985. Thus, it was revealed that the material was polymer with a 162-Da unit size, calculated from the even intervals. In comparison with the mass spectra of the histopathological specimen and authentic materials, the main component coincided with amylopectin rather than amylose. Tandem MS analysis proved that the main components were oligosaccharides. Finally, we confirmed the identification of amylopectin by staining with periodic acid-Schiff and iodine. These results for the first time show the advantages of MALDI-IMS in combination with enzyme digestion for the direct analysis of oligosaccharides as a major component of histopathological samples.     

Structural analysis of (methyl-esterified) oligogalacturonides using post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The use of post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the structural analysis of ((partly) methyl-esterified) oligogalacturonides (oligoGalA) is described. The fragmentation behavior of purified (un)saturated oligoGalA (degree of polymerization 3-6), methyl-esterified and methyl-glycosydated oligoGalA was studied. General fragmentation patterns are described and used for the elucidation of the positions of methyl esters on partly methyl-esterified oligoGalA. This technique now permits the determination of the position of methyl esters or other substituents on pectic fragments, helping in understanding the mode of action of pectinolytic enzymes.     

Sodium-tolerant matrix for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay of oligonucleotides

A mixture of 2',4',6'-trihydroxyacetophenone in acetonitrile and aqueous triammonium citrate solution in a 1:1 molar proportion (0.2 M concentration) was found to be a good matrix for the detection of synthetic oligodeoxynucleotide samples. A high proportion of volatile solvent as well as the high salt content ensure fast co-crystallization of the matrix, co-matrix and analyte molecules. Matrix-assisted laser desorption/ionization (MALDI) mass spectra obtained in negative ion reflectron mode from samples prepared with this protocol show deprotonated molecules [M - H](-), rather than sodium adducts, as the most abundant ions even when up to 50 mM of sodium chloride is present in the sample. The matrix is shown to be effective for low mass modified single nucleotides as well as for longer oligodeoxynucleotides (up to 18mer). Post-source decay (PSD) mass spectra can also be obtained by increasing the laser fluence. Simple sequence information such as the identity and localization of a deleted base or the 5'/3' orientation can then easily be obtained. The calibration method and mass accuracy required are discussed depending on the type of information required.     

Selenium bioaccessibility assessment in selenized yeast after "in vitro" gastrointestinal digestion using two-dimensional chromatography and mass spectrometry

In order to investigate the potentially bioavailable selenium-containing compounds in the selenized yeast candidate reference material SEAS 6, a two-dimensional (size exclusion-reversed phase) chromatography approach has been worked out. Electrospray tandem mass spectrometry (ESI Q-TOF MS) was then used for off-line identification of low molecular weigh selenocompounds generated during the gastrointestinal digestion. Selenomethionine (SeMet) was the major compound identified in the gastrointestinal extract while SeMet selenoxide was its main degradation product formed after medium and long-term sample storage, respectively. Total Se and SeMet were quantified in both the soluble extracts and the residue. Results showed that 89+/-3% of total Se was extracted after gastrointestinal digestion, but only 34+/-1% was surprisingly quantified as free SeMet. The rest of Se was present as many other low, medium and high molecular weight Se-species, which could be detected and further characterized by using the two-dimensional chromatography approach proposed here. Interestingly, most of Se-species seemed to be Se-peptides unspecifically produced by the gastrointestinal juice. These results show for the first time that while the efficiency of human gastrointestinal digestion to dissolve Se-containing proteins present in yeast may be high, its efficiency to convert them into free SeMet is much lower. Se-species present in the insoluble residue (not assimilated by the organism), accounting for 11+/-1% of the total Se in selenized yeast, were also studied. After treatment with SDS (denaturing agent) only 13+/-2% of this "insoluble" Se was solubilized, indicating that it was mainly non-protein bound and likely associated to other insoluble matrix components.     

Determination of photomodified oligodeoxynucleotides by exonuclease digestion, matrix-assisted laser desorption/ionization and post-source decay mass spectrometry

A fast method to detect and sequence photomodified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is reported. Upon treatment of modified ODNs with both phosphodiesterase I and phosphodiesterase II, the digestion stops at the sites of photomodification. Post-source decay (PSD) of MALDI-produced ions from two enzymatic digestion end products distinguishes isomers such as 5'-d(T[cis-syn]TAAGC) and 5'-d(CGAAT[cis-syn]T), which have symmetrical or identical compositions at the 3' and 5' ends, respectively. Studies have also been done to follow the kinetics for enzyme degradation of photomodified ODNs. The calculated rate constants from a mathematical treatment of the time-dependent MALDI data clearly show that the enzymatic digestion rate slows as the enzyme approaches the modified site.     

Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry

Peptide sequencing by mass spectrometry is gaining increasing importance for peptide chemistry and proteomics. However, available tools for interpreting matrix-assisted laser desorption/ionization post-source decay (MALDI-PSD) mass spectra depend on databases, and identify peptides by matching experimental data with spectra calculated from database sequences. This severely obstructs the identification of proteins and peptides not listed in databases or of variations, e.g. mutated proteins. The development of a new computer program for database-independent peptide sequencing by MALDI-PSD mass spectrometry is reported here. This computer program was validated by the determination of the correct sequences for various peptides including sequences listed in the sequence databases, but also for peptides that deviate from database sequences or are completely artificial. This strategy should substantially facilitate the identification of novel or variant peptides and proteins, and increase the power of MALDI-PSD analyses in proteomics.     

Label-free quantification using MALDI mass spectrometry: considerations and perspectives

Profound knowledge of protein abundances in healthy tissues and their changes in disease is crucial for understanding biological processes in basic science and for the development of novel diagnostics and therapeutics. Mass spectrometrybased label-free protein quantification is used increasingly often to gain insights into physiological changes observed in perturbed systems. Although the soft ionization techniques electrospray ionization and matrix-assisted laser desorption/ionization have both been used for protein quantification, this article focuses on instrumental setups with a MALDI ion source. Beside reviewing current bioinformatic data-processing tools for label-free quantification and elaborating on the technical benefits of combining UHPLC and MALDI-MS, we outline the potential of state-of-the-art instruments by reporting unpublished results obtained from twenty-four complex biological samples. This review points out that the capabilities of LC-MALDI MS systems have not yet been fully utilized because of a lack of suitable software tools.