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In this study, we report the use of pyrolysis-GCxGC/MS profiles for an optimized treatment of data issued from pyrolysis-GC/MS combined with the automatic deconvolution software Automated Mass Spectral Deconvolution and Identification System (AMDIS). The method was illustrated by the characterization of marker compounds of East Asian handmade papers through the examination of pyrolysis-GCxGC/MS data to get information which was used for manually identifying low concentrated and co-eluting compounds in 1D GC/MS data. The results showed that the merits of a higher separation power for co-eluting compounds and a better sensitivity for low concentration compounds offered by a GCxGC system can be used effectively for AMDIS 1D GC/MS data treatment: (i) the compound distribution in pyrolysis-GCxGC/MS profiles can be used as “peak finder” for manual check of low concentration and co-eluting compound identification in 1D GC/MS data, and (ii) pyrolysis-GCxGC/MS profiles can provide better quality mass spectra with observed higher match factors in the AMDIS automatic match process. The combination of 2D profile with AMDIS was shown to contribute efficiently to a better characterization of compound profiles in the chromatograms obtained by 1D analysis in focusing on the mass spectral identification.Graphical abstract [ABSTRACT FROM AUTHOR]

Surface treatment of biological tissue sections improves detection of peptides and proteins for mass spectrometry imaging. However, liquid surface treatments can result in diffusion of surface analytes and fragile tissue sections can be easily damaged by typical washing solvents. Here, we present a new surface washing procedure for mass spectrometry imaging. This procedure uses solvent wetted fiber-free paper to enable local washing of tissue sections for mass spectrometry imaging and tissue profiling experiments. In addition, the method allows fragile tissues that cannot be treated by conventional washing techniques to be analyzed by mass spectrometry imaging. [ABSTRACT FROM AUTHOR]

A previous paper considered the problems that presently limit the hydrogen exchange - mass spectrometry (HX-MS) method for studying the biophysical and functional properties of proteins. Many of these problems can be overcome by obtaining and analyzing hundreds of sequentially overlapping peptide fragments that cover the protein many times over (Mayne et al. J. Am. Soc. Mass Spectrom. 2011: ). This paper describes a computer program called ExMS that furthers this advance by making it possible to efficiently process crowded mass spectra and definitively identify and characterize these many peptide fragments. ExMS automatically scans through high resolution MS data to find the individual isotopic peaks and isotopic envelopes of a list of peptides previously identified by MS/MS. It performs a number of tests to ensure correct identification in spite of peptide overlap in both chromatographic and mass spectrometric dimensions and possible multi-modal envelopes due to static or dynamic structural heterogeneity or HX EX1 behavior. The program can automatically process data from many sequential HX time points with no operator intervention at the rate of ~2 sec per peptide per HX time point using desktop computer equipment, but it also provides for rapid manual checking and decision when ambiguity exists. Additional subroutines can provide a step by step report of performance at each test along the way and parameter adjustment, deconvolute isotopic envelopes, and plot the time course of single and multi-modal H-D exchange. The program will be available on an open source basis at: [ABSTRACT FROM AUTHOR]

Measurement of the naturally occurring hydrogen exchange (HX) behavior of proteins can in principle provide highly resolved thermodynamic and kinetic information on protein structure, dynamics, and interactions. The HX fragment separation-mass spectrometry method (HX-MS) is able to measure hydrogen exchange in biologically important protein systems that are not accessible to NMR methods. In order to achieve high structural resolution in HX-MS experiments, it will be necessary to obtain many sequentially overlapping peptide fragments and be able to identify and analyze them efficiently and accurately by mass spectrometry. This paper describes operations which, when applied to four different proteins ranging in size from 140 to 908 residues, routinely provides hundreds of useful unique peptides, covering the entire protein length many times over. Coverage in terms of the average number of peptide fragments that span each amino acid exceeds 10. The ability to achieve these results required the integrated application of experimental methods that are described here and a computer analysis program, called ExMS, described in a following paper. [ABSTRACT FROM AUTHOR]

The orbital trap mass analyzer provides a number of unique analytical features along with inevitable limitations as an electrostatic instrument operating in high space charge regimes resulting in systematic measured frequency errors as an effect of stored ion clouds on the trap field and each other effect of non-ideal machining the trap electrodes, effect of injection slot, effect of real versus theoretical trap dimensions, etc. This paper deals with determining the influence of the space charge effect and imperfection of the electrostatic field on the motion of ion ensembles in the orbital trap. We examine effects of theoretically modeled non-harmonicity of the electrostatic potential and the number of confined ions on stability of coherent ion motion in the trap that determines the frequency shifts of axial ion oscillation. Three different Orbitrap geometries were considered: geometry close to preproduction Orbitrap, close to standard Orbitrap, close to high field Orbitrap. Frequency shifts for m/z = 500 and for charge state +23 of cytochrome c isotopic cluster particles with $$ {10^4} $$-6* $$ {10^6} $$ elemental charges in the trap were considered. Refined spectra were calculated using the filter diagonalization method proposed by Mandelshtam et al. and applied to mass spectrometry by O'Connor and Aizikov. [ABSTRACT FROM AUTHOR]

Achieving (bio)macromolecular structural assignment from the interpretation of ion mobility spectrometry (IMS) experiments requires successful comparison with computer modeling. Replica-exchange molecular dynamics simulations with suitable force fields not only offer a convenient framework to locate relevant conformations, especially in the case of multiple-funnel energy landscapes, but they are also well suited to statistical analyses. In the present paper, we discuss two extensions of the method used to improve its efficiency in the context of IMS. Two doubly-protonated polyalanines [RAXAK + 2H] with X = V and D appear as favorable cases for which the calculated collision cross-section distributions naturally agree with the measurements, providing reliable candidate structures. For these compounds, a careful consideration of other order parameters based on the weighted histogram method resolves several otherwise hidden underlying conformational families. In the case of a much larger peptide exhibiting bistability, assignment is more difficult but could be achieved by guiding the sampling with an umbrella potential using the square gyration radius as the biasing coordinate. Applied to triply protonated bradykinine, the two presented methods indicate that different conformations compatible with the measurements are very close in energy. [ABSTRACT FROM AUTHOR]

The reaction between CO and aqueous amines to produce a charged carbamate product plays a crucial role in post-combustion capture chemistry when primary and secondary amines are used. In this paper, we report the low energy negative-ion CID results for several anionic carbamates derived from primary and secondary amines commonly used as post-combustion capture solvents. The study was performed using the modern equivalent of a triple quadrupole instrument equipped with a T-wave collision cell. Deuterium labeling of 2-aminoethanol (1,1,2,2,-d-2-aminoethanol) and computations at the M06-2X/6-311++G(d,p) level were used to confirm the identity of the fragmentation products for 2-hydroxyethylcarbamate (derived from 2-aminoethanol), in particular the ions CN, NCO and facile neutral losses of CO and water; there is precedent for the latter in condensed phase isocyanate chemistry. The fragmentations of 2-hydroxyethylcarbamate were generalized for carbamate anions derived from other capture amines, including ethylenediamine, diethanolamine, and piperazine. We also report unequivocal evidence for the existence of carbamate anions derived from sterically hindered amines ( Tris(2-hydroxymethyl)aminomethane and 2-methyl-2-aminopropanol). For the suite of carbamates investigated, diagnostic losses include the decarboxylation product (−CO, 44 mass units), loss of 46 mass units and the fragments NCO ( m/z 42) and CN ( m/z 26). We also report low energy CID results for the dicarbamate dianion (OCNHCHNHCO) commonly encountered in CO capture solution utilizing ethylenediamine. Finally, we demonstrate a promising ion chromatography-MS based procedure for the separation and quantitation of aqueous anionic carbamates, which is based on the reported CID findings. The availability of accurate quantitation methods for ionic CO capture products could lead to dynamic operational tuning of CO capture-plants and, thus, cost-savings via real-time manipulation of solvent regeneration energies. [ABSTRACT FROM AUTHOR]

Mass spectrometers that use different types of analyzers for the first and second stages of mass analysis in tandem mass spectrometry (MS/MS) experiments are often referred to as “hybrid” mass spectrometers. The general goal in the design of a hybrid instrument is to combine different performance characteristics offered by various types of analyzers into one mass spectrometer. These performance characteristics may include mass resolving power, the ion kinetic energy for collision-induced dissociation, and speed of analysis. This paper provides a review of the development of hybrid instruments over the last 30 years for analytical applications. [Copyright &y& Elsevier]

This paper, describing electron ionization mass spectral fragmentation of some hydroxycarboxylic and oxocarboxylic acid trimethylsilyl derivatives, focuses on the formation of fragment ions resulting from the interactions between the two functionalities of these compounds. These interactions result in the formation of fragment ions at [CH2 = C(OTMS)2]+·, [CH2 = CHC(OTMS) = OTMS]+, [M − 31]+, [M − 105]+, and [M − RCHO]+· in the case of hydroxycarboxylic acid trimethylsilyl derivatives of formula RCHOTMS(CH2)nCOOTMS and at [RC(OTMS) = CH2]+·, [RC(= OTMS)CH = CH2]+, and [M − RC(= O)CH2]+ in the case of oxocarboxylic acid trimethylsilyl esters of formula RC(= O)(CH2)nCOOTMS. Some of these fragmentations appeared to be sufficiently specific to be used to characterize these compounds. Several fragmentation pathways involving trimethylsilyl and hydrogen transfers were proposed to explain the formation of these different fragment ions and were substantiated by deuterium labeling. [Copyright &y& Elsevier]

In this paper, we report the analysis of seven benzopyridoindole and benzopyridoquinoxaline drugs binding to different duplex DNA and triple helical DNA, using an approach combining electrospray ionization mass spectrometry (ESI-MS), tandem mass spectrometry (MS/MS), and molecular modeling. The ligands were ranked according to the collision energy (CE50) necessary to dissociate 50% of the complex with the duplex or the triplex in tandem MS. To determine the probable ligand binding site and binding mode, molecular modeling was used to calculate relative ligand binding energies in different binding sites and binding modes. For duplex DNA binding, the ligand-DNA interaction energies are roughly correlated with the experimental CE50, with the two benzopyridoindole ligands more tightly bound than the benzopyridoquinoxaline ligands. There is, however, no marked AT versus GC base preference in binding, as supported both by the ESI-MS and the calculated ligand binding energies. Product ion spectra of the complexes with triplex DNA show only loss of neutral ligand for the benzopyridoquinoxalines, and loss of the third strand for the benzopyridoindoles, the ligand remaining on the duplex part. This indicates a higher binding energy of the benzopyridoindoles, and also shows that the ligands interact with the triplex via the duplex. The ranking of the ligand interaction energies compared with the CE50 values obtained by MS/MS on the complexes with the triplex clearly indicates that the ligands intercalate via the minor groove of the Watson-Crick duplex. Regarding triplex versus duplex selectivity, our experiments have demonstrated that the most selective drugs for triplex share the same heteroaromatic core. [Copyright &y& Elsevier]

We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from “zoom scan” data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly- through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution. [Copyright &y& Elsevier]

This paper describes a novel emitter tip having the shape of a nib and based on an open structure for nano-electrospray ionization mass spectrometry (nanoESI-MS). The nib structure is fabricated with standard lithography techniques using SU-8, an epoxy-based negative photoresist. The tip is comprised of a reservoir, a capillary slot and a point-like feature, and is fabricated on a silicon wafer. We present here a novel scheme for interfacing such nib tips to MS by applying the ionization voltage directly onto the semi-conductor support. The silicon support is in direct contact with the liquid to be analyzed at the reservoir and microchannel level, thus allowing easy use in ESI-MS. This scheme is especially advantageous for automated analysis as the manual step of positioning a metallic wire into the reservoir is avoided. In addition, the analysis performance was enhanced compared with the former scheme, as demonstrated by the tests of standard peptides (gramicidin S, Glu-fibrinopeptide B). The limit of detection was determined to be lower than 10−2 μM. Due to their enhanced performance, these microfabricated sources might be of great interest for analysis requiring very high sensitivity, such as proteomics analysis using nanoESI-MS. [Copyright &y& Elsevier]

This paper describes the characterization of low molecular weight components of four materials using electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). The materials in the current study are [(ViMe2SiO1/2)x(PhSiO3/2)y(SiO4/2)z] (MTQ), [(ViMe2SiO1/2)x(SiO4/2)y] (MQ), and [(SiO4/2)x(HO1/2)y(tBuO1/2)z] (Q) silsesquioxanes. Accurate mass measurements coupled with knowledge of resin chemistry afforded siloxane composition determination that was used to propose specific structures for the oligomers. Branched or linear (TnQmMn+2m+2), and monocyclic (TnQmMn+2m) structures are predominant structures for the low molecular weight species in MTQ. For MQ and Q, more condensed structures, such as partially opened cage structures (QmM2m−6 and QmM2m−8), were identified. The differences between MQ, Q, and MTQ are likely attributed to differences in intrinsic structure and reactivity of T and Q building blocks. The structural information obtained for these oligomeric species will ultimately provide a better understanding of new resin materials and their associated physical properties. [Copyright &y& Elsevier]

With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments. [Copyright &y& Elsevier]

The source of discoloration on a polymer surface can often be identified by washing the surface of the discolored polymer to collect the color bodies, then analyzing the washings using liquid chromatography-mass spectrometry (LCMS), with an in-line ultraviolet (UV) detector set at the optimum wavelength for the particular color bodies. A reference sample having no discoloration is also analyzed in the same way. In this paper, results from this methodology are compared with direct time of flight-secondary ion mass spectrometry (TOF-SIMS) analysis of a discolored polymer. The benefits and shortcomings of each methodology are discussed. [Copyright &y& Elsevier]

The present paper suggests a new algorithm for estimation of peak positions in FTMS spectra. It is shown theoretically and experimentally that the new technique yields superior results compared to the currently applied techniques, when the noise level is high and/or the peaks are located close to each other. Cases are presented where the deviation from the true mass could be mistaken for space charge effect, while the shift is in fact solely due to the shortcomings of the current techniques and can be corrected by applying the shifted-basis technique. In two out of three cases, this technique gave more accurate (>5 times) result compared to the conventional analysis. In the third case, where the signal was high compared to the noise, the results were comparable. The new technique can be used to achieve better mass accuracy for noisy and not well resolved spectra, and to further investigate the features of the space charge effect. [Copyright &y& Elsevier]

Metal-assisted (MetA) static secondary ion mass spectrometry (S-SIMS) is one of several ion yield enhancing methods developed for S-SIMS in the last decades. MetA-S-SIMS uses a very thin coating of gold or silver on the sample. Earlier experiments revealed dependence of the ion yield enhancement on the applied metal, the nature of the studied sample, the time after metallization, and the heating temperature (ex situ, i.e., under atmospheric pressure). This paper reports on the effects of time and temperature when samples are heated to temperatures between 30 and 80°C inside the S-SIMS vacuum chamber (in situ). Thick layers of poly(vinylbutyral-co-vinylalcohol-co-vinylacetate) (PVB) containing dihydroxybenzophenone (DHBPh) were coated with a nm-thin-layer of gold. The S-SIMS analysis was performed over a period of several hours while samples were kept at a constant elevated temperature. Compared to ex situ heating in an oven, heating in the analysis chamber provided more rapid signal enhancement, but the magnitude of the enhancement was less (by a factor of two). Furthermore, additional experiments on ex situ heated samples revealed that storage of samples with enhanced ion yields at −8°C is not sufficient to “stabilize” the enhancement. A steep decrease of the ion yields was observed as a function of time after 2.5 h. [Copyright &y& Elsevier]