Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions

High mass-resolving power has been shown to be useful for studying the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange. A computer algorithm was developed that automatically identifies peptides and their extent of deuterium incorporation from H/D exchange mass spectra of enzymatic digests or fragment ions produced by collisionally induced dissociation (CID) or electron capture dissociation (ECD). The computer algorithm compares measured and calculated isotopic distributions and uses a fast calculation of isotopic distributions using the fast Fourier transform (FFT). The algorithm facilitates rapid and automated analysis of H/D exchange mass spectra suitable for high-throughput approaches to the study of peptide and protein structures. The algorithm also makes the identification independent on comparisons with undeuterated control samples. The applicability of the algorithm was demonstrated on simulated isotopic distributions as well as on experimental data, such as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin peptic digests, and CID and ECD spectra of substance P.     

Automatic recalibration and processing of tandem mass spectra using formula annotation

High accuracy, high resolution tandem mass spectrometry (MS/MS) is becoming more common in analytical applications, yet databases of these spectra remain limited. Databases require good quality spectra with sufficient compound information, but processing, calibration, noise reduction and retrieval of compound information are time‐consuming tasks that prevent many contributions. We present a comprehensive workflow for the automatic processing of MS/MS using formula annotation for recalibration and cleanup to generate high quality spectra of standard compounds for upload to MassBank ( www.massbank.jp ). Compound information is retrieved via Internet services. Reference standards of 70 pesticides were measured at various collision energies on an LTQ‐Orbitrap XL to develop and evaluate the workflow. A total of 944 resulting spectra are now available on MassBank. Evidence of nitrogen adduct formation during MS/MS fragmentation processes was found, highlighting the benefits high accuracy MS/MS offers for spectral interpretation. A database of recalibrated, cleaned‐up spectra resulted in the most correct spectra ranked in first place, regardless of whether the search spectra were recalibrated or not, whereas the average rank of the correct molecular formula was improved from 2.55 (uncalibrated) to 1.53 when using recalibrated MS/MS data. The workflow is available as an R package RMassBank capable of generating MassBank records from raw MS and MS/MS data and can be adjusted to process data acquired with different settings and instruments. This workflow is a vital step towards addressing the need for more high quality, high accuracy MS/MS spectra in spectral databases and provides important information for spectral interpretation. Copyright © 2012 John Wiley & Sons, Ltd.     

HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry

Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.     

Computer aided processing of laser microprobe mass spectra

This article describes the development and subsequent application of a computer aided method, based on the library search strategy, for the interpretation of laser microprobe mass analysis (LAMMA) spectra. Such a routine is essential whenever huge amounts of spectra are needed to obtain relevant results, as e.g. in environmental research. The main handicap for a straightforward automation is the poor reproducibility of the analytical technique.     

Identification of unknown compounds using data bases and computer simulation of mass spectra

The possibility of identification based on the comparison of experimental electron-ionization mass spectrum of an unknown (in our case, model) compound with the mass spectra of the candidate compounds generated by the Mass Frontier software has been demonstrated by the example of three model compounds. The structural isomers of the identified substances found in the ChemExper database have been used as the candidate compounds. The candidate substances have been ranged by the degree of similarity between their simulated mass spectra and the experimental mass spectrum of the unknown compound. The mass spectra have been compared on the basis of the algorithm used in the NIST MS Search standard search system. In all three cases, the sought-after structure has been indicated as the most probable one of all the candidate structures.     

Automated accurate mass data processing using a gas chromatograph/time-of-flight mass spectrometer in drug discovery

A gas chromatograph/time-of-flight (GCT) mass spectrometer, with high mass measurement accuracy to within 5 ppm, has been used for the automated accurate mass analysis of multicomponent mixtures and drug discovery compounds. A multicomponent mixture was analyzed several times over the course of a week to assess the reproducibility and ruggedness of the automated method while operating the GCT in electron ionization mode. For example, the data for 31 radical cations generated via electron ionization was processed using automated software (i.e. OpenLynx) to provide for mass accuracies less than 5 ppm for nearly 100% of the ions from multiple injection data. Mass accuracies of the radical anions of polyaromatic hydrocarbons generated via negative chemical ionization, and protonated pyridines and quinolines generated via methane chemical ionization, were mainly less than 5 ppm from multiple injection data. In addition, the automated method has been used for the accurate mass analysis of drug discovery compounds.     

Methyl guanine isomer distinction by hydrogen / deuterium exchange using a fourier transform mass spectrometer

Analytical Chemistry Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Differentiation of the seven isomers of methyl guanine has been accomplished by monitoring gas-phase hydrogen/deuterium (H/D) exchange reactions of the protonated molecular ions with deuterium oxide (D₂O) in a Fourier transform mass spectrometer. In each case a distinctive reaction rate for the first H/D exchange was observed, and exchanges of up to three deuterium atoms occurred with characteristic ion abundances that could be used to differentiate the isomers. O⁶-Methyl guanine, for example, showed only one slow H/D exchange with D₂O, whereas l-methyl guanine exchanged two hydrogen atoms at a significantly faster rate. On comparison of the possible resonance structures of each protonated isomer with the experimental information about the number and rate of H/D exchanges observed, a reaction mechanism involving a concerted proton abstraction-deuterium cation donation was proposed.     

Analysis of protein complexes with hydrogen exchange and mass spectrometry

Analysis of protein complexes using hydrogen exchange (HX) combined with high resolution electrospray mass spectrometry (MS) is demonstrated. HX MS offers the possibility to analyze the strength of binding in protein complexes, to identify regions that undergo binding induced structural changes, and to study the nature (hydrophobic, electrostatic, etc.) of binding between two or more proteins. In the current work, a heteromeric complex containing UBC9 (an E2 conjugating enzyme) and SUMO-1 (a ubiquitin-like modifier) was investigated by incubating the complex in D2O and measuring the amount of deuterium incorporation with MS. SUMO-1 had significant changes in deuterium levels when bound to UBC9. In contract, few or no changes in deuterium levels were detected in UBC9 when part of the complex, even at the binding interface. Titrations were used to estimate the binding constant for the complex. The nature of the interface was probed by creating a site-directed mutant form of UBC9. The mutant form showed no detectable binding to SUMO-1 and thereby suggested that binding between these two proteins is primarily electrostatically driven. This application of HX MS demonstrates its value in the study of protein complexes and protein machinery.     

Design and development of a new program for data processing of mass spectra acquired by means of a high-resolution double-focusing glow-discharge mass spectrometer

An new program has been developed and implemented for data analysis of mass spectra obtained by use of the VG9000 glow-discharge mass spectrometer. The program, designed to run in a Windows 9X environment includes several tools for import and export of data, cluster generators, etc. An automated technique for the interpretation of mass spectra is also built into the program; this enables faster and operator-independent interpretation. When major interferences or not-well defined signals are involved, the automated technique might fail to find the correct result. Therefore, a manual, VG9000 software-like, bypass is at hand. A comparison of the different techniques and programs shows, in general, comparable results. An installable version of the software is available on the university FTP-server (ftp://PLASMA-FTP.uia.ac.be/ private/imsas/).     

Design and development of a new program for data processing of mass spectra acquired by means of a high-resolution double-focusing glow-discharge mass spectrometer

An new program has been developed and implemented for data analysis of mass spectra obtained by use of the VG9000 glow-discharge mass spectrometer. The program, designed to run in a Windows 9X environment includes several tools for import and export of data, cluster generators, etc. An automated technique for the interpretation of mass spectra is also built into the program; this enables faster and operator-independent interpretation. When major interferences or not-well defined signals are involved, the automated technique might fail to find the correct result. Therefore, a manual, VG9000 software-like, bypass is at hand. A comparison of the different techniques and programs shows, in general, comparable results. An installable version of the software is available on the university FTP-server (ftp://PLASMA-FTP.uia.ac.be/ private/imsas/).     

Computer-assisted prediction of pesticide substructure using mass spectra

Mass spectral classifiers of 16 substructures that are present in basic structures of pesticides have been investigated to assist pesticide residues analysis as well as screening of pesticide lead compounds. Mass spectral data are first transformed into 396 features, and then Genetic Algorithm-Partial Least Squares (GA-PLS) as a feature selection method and Support Vector Machine (SVM) as a validation method are implemented together to get an optimization feature set for each substructure. At last, a statistical method which is AdaBoost algorithm combined with Classification and Regression Tree (AdaBoost-CART) is trained to predict the 16 substructures presence/absence using the optimization mass spectral feature set. It is demonstrated that the optimum feature sets can be used to predict the 16 pesticide substructures presence/absence with mostly 85-100% in recognition success rate instead of the original 396 features.     

Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis

The performance of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks in wheat variety classification is further evaluated.1 Two principal issues were studied: (a) the number of varieties that could be classified correctly; and (b) various means of pre-processing mass spectrometric data. The number of wheat varieties tested was increased from 10 to 30. The main pre-processing method investigated was based on Gaussian smoothing of the spectra, but other methods based on normalisation procedures and multiplicative scatter correction of data were also used. With the final method, it was possible to classify 30 wheat varieties with 87% correctly classified mass spectra and a correlation coefficient of 0.90.     

Solution-phase deuterium/hydrogen exchange at a specific residue using nozzle-skimmer and electron capture dissociation mass spectrometry

Information about protein conformation can be obtained with hydrogen/deuterium exchange (HDX) mass spectrometry. The isotopic solution-phase exchange of specific amide hydrogen atoms can be followed using low-vacuum nozzle-skimmer collision-induced dissociation (CID). In this study, the nozzle-skimmer technique was complemented by electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The solution-phase exchange at a specific residue is monitored by comparing isotopic distributions of two consecutive b- or c-type ions. While nozzle-skimmer fragmentation takes place in the low-vacuum region of the mass spectrometer, ECD occurs at ultra-high vacuum within the mass analyzer cell of the FTICR mass spectrometer. The dissociations take place at 10(-4) and 10(-9) mbar, respectively. Low-vacuum nozzle-skimmer fragmentation can result in intramolecular exchange between product ions and solvent molecules in the gas phase. Consequently, the solution-phase information about protein or peptide conformation is lost. It was not possible to monitor isotopic solution-phase exchange at the eighth residue in substance P, (Phe)8, with nozzle-skimmer CID. By using the in-cell ECD fragmentation method, the solution-phase exchange at the (Phe)8 residue was preserved during mass spectrometric analysis. This result shows the complementary aspects of applying fragmentation at low and at high vacuum, when studying isotopic exchange in solution at specific residues using FTICRMS.     

'On-the-fly' hydrogen/deuterium exchange liquid chromatography/mass spectrometry using a dual-sprayer atmospheric pressure ionisation source

In-source 'on-the-fly' hydrogen/deuterium (H/D) exchange liquid chromatography mass spectrometry (LC/MS) has been investigated. The work was performed using a dual-sprayer source. The analyte was introduced through an electrospray ionisation sprayer and D2O was introduced through an atmospheric pressure chemical ionisation sprayer. To achieve H/D exchange sufficient to determine the number of exchangeable H atoms of a compound, a saturated 'steady-state' D2O atmosphere had to be created in the ion source by having a 2:1 or higher D2O-to-analyte flow rate ratio. Under these conditions H/D exchange levels of 32-90% were achieved. In most cases the H/D exchange was sufficient to measure the number of exchangeable H atoms in some antiulcerative and anthelmintic pharmaceuticals. The concept of in-source 'on-the-fly' H/D exchange by introducing the deuterating agent via a second sprayer has been shown. It allows the integrity of the chromatographic separation to be kept, since the H/D exchange takes place post-separation.     

Studying protein-carbohydrate interactions by amide hydrogen/deuterium exchange mass spectrometry

Protein-carbohydrate interactions play a significant role in biological processes. Presented here is the novel application of amide hydrogen/deuterium exchange mass spectrometry (amide exchange-MS) to the study of the interaction between a protein and its carbohydrate substrate. The degree of deuterium incorporation into hen egg lysozyme was monitored with and without substrate to verify that a carbohydrate can provide sufficiently stable protection of the amide hydrogen atoms in a protein's backbone from exchange with deuterated solvent. The substrate protected a number of amide hydrogens from exchange, implying that protein-carbohydrate binding systems will be compatible with amide exchange-MS. Endopolygalacturonase-II (EPG-II) from Aspergillus niger, a pectin-degrading enzyme, was chosen as the first carbohydrate-binding system to be extensively studied using quenched amide exchange-MS. Monitoring the changes in deuterium incorporation of EPG-II in the presence and absence of an oligomer of galacturonic acid implied the location of substrate binding. This study demonstrates the ability of amide exchange-MS to investigate protein-carbohydrate interactions.     

Charge exchange using a double quadrupole mass spectrometer

Charge exchange mass spectra obtained on a double quadrupole (QQ) mass spectrometer are compared with those obtained by other methods. The effects of reagent ion recombination energies and of axial ion translational energy on these spectra are followed.     

Decomposition of multicomponent mass spectra using Bayesian probability theory

We present a method for the decomposition of the mass spectra of mixed gases using Bayesian probability theory. The method works without any calibration measurement and therefore applies also to the analysis of spectra containing unstable species. For the example of mixtures of three different hydrocarbon gases the algorithm provides concentrations and cracking coefficients of each mixture component and also their confidence intervals. The amount of information needed to obtain reliable results and its relation to the accuracy of our analysis are discussed.