Isomeric identification by laser control mass spectrometry

The influence shaped femtosecond laser pulses have on molecular photofragmentation and ionization, coupled with the intrinsic sensitivity of mass spectrometry, results in a powerful tool for fast, accurate, reproducible and quantitative isomeric identification. Complex phase functions are introduced to enhance differences during the laser-molecule interactions, which depend on geometric structure, resulting in different fragmentation fingerprints. A full account is given on the setup and results leading to a technique that can be used to distinguish between compounds normally indistinguishable by conventional electron ionization mass spectrometry. We demonstrate geometric and structural isomer identification of cis-/trans-3-heptene, cis-/trans-4-methyl-2-pentene, o-/p-cresol and o-/p-xylene. For the positional isomers of xylene we present a complete dataset consisting of 1024 different phases to explore phase complexity. A selection of two phases from that data can then be used to achieve quantitative identification in mixtures of xylene isomers. Finally, we evaluate receiver operational curves obtained from our experimental data to demonstrate the reliability that can be achieved by femtosecond laser control mass spectrometry.     

Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of protein samples from two-dimensional (2-D) gels in conjunction with protein sequence database searches is frequently used to identify proteins. Moreover, the automatic analysis of complete 2-D gels with hundreds and even thousands of protein spots ("proteome analysis") is possible, without human intervention, with the availability of highly accurate mass spectrometry instruments, and high-throughput facilities for preparation and handling of protein samples from 2-D gels. However, the lack of software for precise automatic analysis and annotation of mass spectra, as well as software for in-batch sequence database queries, is increasingly becoming a significant bottleneck for the proteomics work flow. In the present paper we outline an algorithm for reliable, accurate, and automatic evaluation of mass spectrometric data and database searches. We show here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false-positive results. Reliable protein identification is dependent on several parameters: the accuracy of fragment mass determination, the number of masses submitted for query, the mass distribution of query masses, the number of masses matching between sample and database protein, the size of the sequence database, and the kind and number of modifications considered. Using these parameters, we derive a simple statistical estimation that can be used to calculate the probability of true-positive protein identification.     

MALDI-TOF mass spectrometric identification of dyes and pigments

We have used MALDI-TOF mass spectrometry to characterize a selection of dyes from the Schweppe dye collection and pigments from the Tate Gallery collection. MALDI-TOF mass spectra of such samples are easily obtained and, through observation of both positive and negative ion spectra, provide a convenient, versatile method for dye characterization and identification. Such pairs of positive and negative ion spectra immediately distinguish between acidic and basic dyes and provide the characteristic mass of either the molecular ion or a simply related fragment ion. This approach is especially useful in situations where very small amounts of analyte are available, as in museum research and forensic analysis. In the case of textile dyes, we have carried out identification on material from single fibers and, with insoluble pigments, have begun to identify components of historically important pastel sticks from submicrogram samples.     

Matrix-assisted laser desorption/ionization directed nano-electrospray ionization tandem mass spectrometric analysis for protein identification

In those cases where the information obtained by peptide mass fingerprinting or matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) is not sufficient for unambiguous protein identification, nano-electrospray ionization (nano-ESI) and/or electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis must be performed. The sensitivity of nano-ESI/MS, however, is lower than that of MALDI-MS, especially at very low analyte concentrations and/or in the presence of contaminants, such as salt and detergents. Moreover, to perform ESI-MS/MS, the peptide masses of the precursor ions must be known. The approach described in this paper, MALDI-directed nano-ESI-MS/MS, makes use of information obtained from the more sensitive MALDI-MS experiments in order to direct subsequent nano-ESI-MS/MS experiments. Peptide molecular ions found in the MALDI-MS analysis are then selected, as their (+2) precursor ions, for nano-ESI-MS/MS sequencing, even though these ions cannot be detected in the ESI-MS spectra. This method, originally proposed by Tempst et al. (Anal. Chem. 2000, 72: 777-790), has been extended to provide better sensitivity and shorter analysis times; also, a comparison with liquid chromatography/tandem mass spectrometry (LC/MS/MS) has been performed. These experiments, performed using quadrupole time-of-flight instruments equipped with commercially available nano-ESI sources, have allowed the unambiguous identification of in-gel digested proteins at levels below their ESI-MS detection limits, even in the presence of salts and detergents.     

Chromatographic separation and mass spectrometric identification of positional isomers of polyethylene glycol-modified growth hormone-releasing factor (1-29)

A one-step chromatographic method capable of separating all isomers of polyethylene glycol (PEG)-growth hormone-releasing factor (GRF) (1-29) conjugates was developed. The unmodified GRF (1-29) and seven different isomers of PEG-GRF (1-29) conjugates were separated by using a simple reversed-phase HPLC method depending on the differences of hydrophobicity due to the number and site of PEG attachment. The PEGylation sites of all isomers of PEG-GRF (1-29) conjugates were identified by determining the molecular masses of the Lys-C digested fragments with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This study is a first report for the separation of all PEG-conjugate isomers and would be useful for further studies to find the promising conjugate by evaluating biological activity and stability of each isomer.     

Mass spectrometric identification of double bond positional isomers of hexadecenyl acetate without chemical derivatization

A method for the identification of the double bond positional isomers of hexadecenyl acetate has been established by analysing similarity of the mass spectra patterns on a fuzzy classification, in which the intensity ratios of six diagnostic pairs of the predominant ions were selected as standard parameters for the characterization of the double bond position. The procedure was tested with △2 to △15-isomers of chemically unmodified hexadecenyl acetate, and the original double bond position in the acetates was located unambiguously.     

Systematic identification of N-acetylheparosan oligosaccharides by tandem mass spectrometric fragmentation

Recently, a useful procedure for the preparation of both even- and odd-numbered series of N-acetylheparosan (NAH) oligosaccharides was established. The present report describes findings when these NAH oligosaccharides were subjected to comparative mass spectrometry (MS)/MS fragmentation analysis by matrix-assisted laser desorption/ionization (MALDI)-LIFT-time-of-flight (TOF)/TOF-MS/MS, and electrospray ionization (ESI) collision-induced dissociation (CID) MS/MS. The resultant fragment ions were systematically assigned to elucidate fragmentation characteristics. In the MALDI-LIFT-MS/MS experiments, all the NAH oligosaccharides underwent unique glycosidic cleavages that included B-Y ion cleavages (nomenclature system of Domon and Costello, Glycoconjugate J. 1988; 5: 397) at the C-1 side, and C-Z ion cleavages at the C-4 side, with respect to glucuronic acid (GlcA). In addition, (0,2)A and/or (0,2)X cross-ring cleavages were observed for relatively small oligosaccharides. The former observation clearly reflects the occurrence of a GlcA-N-acetylglucosamine (GlcNAc) alternating structure of NAH, while the latter feature implies the occurrence of the -beta-1-4-glucuronide linkage. Extensive glycosidic cleavages were also observed in the ESI-CID-MS/MS fragmentation, though cleavage specificity was less evident than in the case of MALDI-LIFT-TOF/TOF-MS/MS. The information obtained in this study should be valuable for understanding both biosynthetic and degradation processes of NAH and its derivatives including heparin and heparan sulfate, as well as artificially modified NAH oligosaccharides.     

High-performance liquid chromatographic mass spectrometric identification of the photoproducts of cymoxanil

The photochemical degradation of the fungicide cymoxanil {2-cyano-N-[(ethylamino)carbonyl]-2-(methoxyimino) acetamide} was studied in aqueous buffer solution (pH 5.9+/- 0.1) under UV light and in laboratory conditions. The degradation followed a pseudo- first-order kinetic with significant correlation coefficient. The main photoproducts were separated and tentatively identified by HPLC/UV and HPLC/MS data, as 3-ethyl-4-(methoxyamino)-2,5-dioxo-4-imidazolidinecarbonitrile, 1-ethyl-5-(methoxyimino)-2,4-imidazolidin-2,4-dione, ethylimidazolidinetrione and {[(ethylamino)carbonyl]-amino}oxoacetic acid. A photolysis pathway of cymoxanil is proposed.     

Dansylation of tryptic peptides for increased sequence coverage in protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric peptide mass fingerprinting

A database search using peptide mass fingerprints obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry leads to protein identification with incomplete sequence coverage, because certain peptides are preferentially desorbed/ionized and some are not detected at all. We show that certain tryptic peptides mainly with C-terminal arginine not detected before derivatization become detectable upon dansylation. Others, mainly with C-terminal lysine, are suppressed. An increase in protein sequence coverage and protein identification score by combined data from underivatized and dansylated peptides in database search is demonstrated using human amnion proteins (human serum albumin precursor, calmodulin, collagen alpha 2(VI) chain precursor, galectin-3) separated by two-dimensional gel electrophoresis as well as femtomole amounts of BSA in solution.     

A mass spectrometric study of the adducts of acetylacetone and cyanogen (Traube's isomers)

The mass spectrometric behaviour of the title compounds has been studied in detail with the aid of deuterium labelling, exact mass measurements, linked scans and collisionally activated decomposition experiments. An interesting conversion reaction of the cyanoenaminedione isomer into the corresponding furane derivative, which appears complete in the second field free region, has been thoroughly investigated.     

A 193 nm laser photofragmentation time-of-flight mass spectrometric study of chloroiodomethane

The photodissociation dynamics of chloroiodomethane (CH2ICl) at 193 nm has been investigated by employing the photofragment time-of-flight (TOF) mass spectrometric method. Using tunable vacuum ultraviolet undulator synchrotron radiation for photoionization sampling of nascent photofragments, we have identified four primary dissociation product channels: CH2Cl + I(2P(1/2))/I(2P(3/2)), CH2I + Cl(2P(1/2))/Cl(2P(3/2)), CHI + HCl, and CH2 + ICl. The state-selective detection of I(2P(3/2)) and I(2P(1/2)) has allowed the estimation of the branching ratio for I(2P(1/2)):I(2P(3/2)) to be 0.73:0.27. Theoretical calculations based on the time-dependent density-functional theory have been also made to investigate excited electronic potential-energy surfaces, plausible intermediates, and transition structures involved in these photodissociation reactions. The translation energy distributions derived from the TOF measurements suggest that at least two dissociation mechanisms are operative for these photodissociation processes. One involves the direct dissociation from the 2 1A' state initially formed by 193 nm excitation, leading to significant kinetic-energy releases. For the I-atom and Cl-atom elimination channels, the fragment kinetic-energy releases observed via this direct dissociation mechanism are consistent with those predicted by the impulsive dissociation models. Other mechanisms are likely predissociative or statistical in nature from the lower 1 1A' and 1 1A' states and/or the ground X 1A' state populated by internal conversion from the 2 1A' state. On the basis of the maximum kinetic-energy release for the formation of CH2Cl + I(2P(1/2)), we have obtained a value of 53+/-2 kcal/mol for the 0 K bond dissociation energy of I-CH2Cl. The intermediates and transition structures for the CHI + HCl and CH2 + ICl product channels have been also investigated by ab initio quantum calculations at the MP2(full)/6-311G(d) and B3LYP(full)/6-11G(d) levels of theory. The maximum kinetic-energy releases observed for the CHI + HCl and CH2 + ICl channels are consistent with the interpretation that the formation of CHI and CH2 in their ground triplet states is not favored.     

Structural identification of alkene isomers by photodissociation–photoionization mass spectrometry

Photodissociation-photoionization, mass spectrometry (PDPI/MS) is used to probe the neutral dissociation chemistry of branched alkenes and dienes. Molecules are photodissociated with an ultraviolet laser and the resulting neutral fragments are subsequently photoionized with coherent vacuum ultraviolet radiation. The neutral fragmen tation observed is useful for characterizing compounds which isomerize prior to ionic fragmentation. Unimolecular photodissociation of dienes and branched alkenes is dominated by cleavage of the β C? C bond. In a few cases, α-cleavage is also observed. When two isomers produce isomass primary products, secondary fragmentation can be used to distinguish the structures. The primary and secondary product distributions are predictable and usually occur without iomerization. As a result, PDPI/MS can be used to determine the sites of branching and unsaturation in small (C₅–C₈) aliphatic compounds.     

Efficient enrichment and identification of phosphopeptides by cerium oxide using on-plate matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis

An efficient and simple method for enrichment and identification of phosphopeptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using cerium oxide is presented. After pretreatment of tryptic digests of phosphoproteins with CeO(2), nonphosphopeptides are discarded and phosphopeptides are enriched. By applying the separated CeO(2) on a target plate and analysis using MALDI-TOF MS, peaks of phosphopeptides and their correspondingly series of dephosphorylated peptides are observed in the mass spectra. Thus, the phosphopeptides are very easy to identify with the mass difference, which are all 80 Da between adjacent peaks in the same series, and clear background in the spectra owing to elimination of signal suppression from large amounts of nonphosphopeptides. Furthermore, the phosphopeptides can be dephosphorylated completely after a further NH(4)OH elution. Tryptic digest products from several standard proteins are pretreated using CeO(2) to demonstrate the efficiency of this method. Phosphopeptides from a very small quantity of human serum are enriched and analyzed, and proteins also identified by searching against a database using Mascot on MALDI-TOF/TOF fragments, which indicates that this method may be employed in complex samples for further application.     

Liquid chromatography-electrospray mass spectrometric identification of ginsenosides in Panax ginseng roots.

A high-performance liquid chromatographic method was developed for electrospray mass spectrometric analysis of ginsenosides in Panax ginseng roots. The analyses were performed on a reversed-phase C18 column using a binary eluent (aqueous 8 mM NH4OAc, buffered to pH 7 with NH4OH-acetonitrile) under gradient conditions. Twenty-five ginsenosides could be separated and detected. The mass spectra obtained provided information on their molecular masses. A MS-MS experiment was undertaken in order to determine the sugar unit sequences and the aglycone moieties.     

Gas chromatographic-tandem mass spectrometric identification of phenolic compounds in Sicilian olive oils

Phenolic compounds in Sicilian olive oils were analyzed by GC-MS and GC-MS/MS after extraction with methanol:water 80:20 and derivatization with bis(trimethylsilyl)trifluoracetamide and trimethylchlorosilane (BSTFA:TMCS 99:1). Numerous compounds were detected and 23 were identified. Tyrosol, hydroxytyrosol and the decarbomethoxy ligstroside and oleuropein aglycons in the dialdehydic forms were the most abundant compounds. 4-(Acetoxyethyl)-1-hydroxybenzene, 3,4-dihydroxyphenylacetaldehyde, syringaldehyde and the cis form of ferulic acid were identified: these compounds were not found in olive oils before. The presence of the dialdehydic form of elenolic acid (without carbomethoxy group) linked to 3-methoxy-4-hydroxyphenylethanol was hypothesized. There were quantitative differences in oils from the varieties Nocellara del Belice, Santagatese and Cerasuola; these differences could depend on the olive varieties and ripeness.