The critical evaluation of a comprehensive mass spectral library

Metabonomic profiling of bladder cancer

Early diagnosis and life-long surveillance are clinically important to improve the long-term survival of bladder cancer patients. Currently, a noninvasive biomarker that is as sensitive and specific as cystoscopy in detecting bladder tumors is lacking. Metabonomics is a complementary approach for identifying perturbed metabolic pathways in bladder cancer. Significant progress has been made using modern metabonomic techniques to characterize and distinguish bladder cancer patients from control subjects, identify marker metabolites, and shed insights on the disease biology and potential therapeutic targets. With its rapid development, metabonomics has the potential to impact the clinical management of bladder cancer patients in the future by revolutionizing the diagnosis and life-long surveillance strategies and stratifying patients for diagnostic, surgical, and therapeutic clinical trials. An introduction to metabonomics, typical metabonomic workflow, and critical evaluation of metabonomic investigations in identifying biomarkers for the diagnosis of bladder cancer are presented.

Loss of H2 and CO from protonated aldehydes in electrospray ionization mass spectrometry

RATIONALE

Electrospray ionization mass spectrometry (ESI-MS) of many protonated aldehydes shows loss of CO as a major fragmentation pathway. However, we find that certain aldehydes undergo loss of H2 followed by reaction with water in the collision cell. This complicates interpretation of tandem mass (MS/MS) spectra and affects multiple reaction monitoring (MRM) results.

METHODS

3-Formylchromone and other aldehydes were dissolved in acetonitrile/water/formic acid and studied by ESI-MS to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, ion trap (IT), and Orbitrap HCD). Certain product ions were found to react with water and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. Theoretical calculations were performed to help with the interpretation of the fragmentation mechanism.

RESULTS

Protonated 3-formylchromones and 3-formylcoumarins undergo loss of H2 as a major fragmentation route to yield a ketene cation, which reacts with water to form a protonated carboxylic acid. In general, protonated aldehydes which contain a vicinal group that forms a hydrogen bridge with the formyl group undergo significant loss of H2. Subsequent losses of CO and C3O are also observed. Theoretical calculations suggest mechanistic details for these losses.

CONCLUSIONS

Loss of H2 is a major fragmentation channel for protonated 3-formychromones and certain other aldehydes and it is followed by reaction with water to produce a protonated carboxylic acid, which undergoes subsequent fragmentation. This presents a problem for reference libraries and raises concerns about MRM results.

Quantitative detection of trace explosive vapors by programmed temperature desorption gas chromatography-electron capture detector

The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive vapor samples. The direct liquid deposition method yields a higher fidelity between the analysis of vapor samples and the analysis of solution standards than using separate injection methods for vapors and solutions, i.e., samples collected on vapor collection tubes and standards prepared in solution vials. Additionally, the method can account for instrumentation losses, which makes it ideal for minimizing variability and quantitative trace chemical detection. Gas chromatography with an electron capture detector is an instrumentation configuration sensitive to nitro-energetics, such as TNT and RDX, due to their relatively high electron affinity. However, vapor quantitation of these compounds is difficult without viable vapor standards. Thus, we eliminate the requirement for vapor standards by combining the sensitivity of the instrumentation with a direct liquid deposition protocol to analyze trace explosive vapor samples.

Quality control for building libraries from electrospray ionization tandem mass spectra

Electrospray ionization (ESI) tandem mass spectrometry coupled with liquid chromatography is a routine technique for identifying and quantifying compounds in complex mixtures. The identification step can be aided by matching acquired tandem mass spectra (MS(2)) against reference library spectra as is routine for electron ionization (EI) spectra from gas chromatography/mass spectrometry (GC/MS). However, unlike the latter spectra, ESI MS(2) spectra are likely to originate from various precursor ions for a given target molecule and may be acquired at varying energies and resolutions and have characteristic noise signatures, requiring processing methods very different from EI to obtain complete and high quality reference spectra for individual analytes. This paper presents procedures developed for creating a tandem mass spectral library that addresses these factors. Library building begins by acquiring MS(2) spectra for all major MS(1) peaks in an infusion run, followed by assigning MS(2) spectra to clusters and creating a consensus spectrum for each. Intensity-based constraints for cluster membership were developed, as well as peak testing to recognize and eliminate suspect peaks and reduce noise. Consensus spectra were then examined by a human evaluator using a number of criteria, including a fraction of annotated peaks and consistency of spectra for a given ion at different energies. These methods have been developed and used to build a library from >9000 compounds, yielding 230,000 spectra.

Facile Smiles-type rearrangement in radical cations of N-acyl arylsulfonamides and analogs

RATIONALE

N-Alkylation of sulfonylbenzamides was reported recently to cause a dramatic and surprising change in electron ionization mass spectrometry (EIMS), leading to a closed-shell base peak. Only an incomplete, speculative mechanism was available at that time. The fragmentation mechanism is determined in the present work and set in the context of related compounds.

METHODS

Candidate reaction mechanisms were evaluated theoretically using modest density-functional calculations. The fragmentation mechanism with the lowest barriers was identified and one of its implications tested successfully by experimental (18) O-isotopic substitution.

RESULTS

The amide oxygen atom attacks the arylsulfonyl group at the ipso position (Smiles-type rearrangement), displacing a molecule of SO2 . The resulting carboximidate radical cation has a weak C-O bond that breaks easily. The incipient aryloxyl radical abstracts a proton from the amide nitrogen to form the dominant product ion, but if the molecule is N-alkylated this cannot occur. Instead, the neutral aryloxyl radical is lost and a closed-shell, N-alkyl nitrilium ion is the major product.

CONCLUSIONS

The Smiles-type ion fragmentation mechanism is facile for the title compounds, despite the necessity for carbonyl oxygen to serve as a nucleophile. This rearrangement probably occurs in many of the mass spectra reported for structurally similar compounds, in which the nucleophile may be a thione, arylthio, imine, methylene, or methine moiety.

Isotopically nonstationary MFA (INST-MFA) of autotrophic metabolism

Metabolic flux analysis (MFA) is a powerful approach for quantifying plant central carbon metabolism based upon a combination of extracellular flux measurements and intracellular isotope labeling measurements. In this chapter, we present the method of isotopically nonstationary (13)C MFA (INST-MFA), which is applicable to autotrophic systems that are at metabolic steady state but are sampled during the transient period prior to achieving isotopic steady state following the introduction of (13)CO2. We describe protocols for performing the necessary isotope labeling experiments, sample collection and quenching, nonaqueous fractionation and extraction of intracellular metabolites, and mass spectrometry (MS) analysis of metabolite labeling. We also outline the steps required to perform computational flux estimation using INST-MFA. By combining several recently developed experimental and computational techniques, INST-MFA provides an important new platform for mapping carbon fluxes that is especially applicable to autotrophic organisms, which are not amenable to steady-state (13)C MFA experiments.

Isotopomer measurement techniques in metabolic flux analysis II: mass spectrometry

Mass spectrometry (MS) offers a sensitive, reliable, and highly accurate method for measurement of isotopic labeling, which is required for generating comprehensive flux maps using metabolic flux analysis (MFA). We present protocols for assessing isotope labeling in a wide range of biochemical species, including proteinogenic amino acids, free organic and amino acids, sugar phosphates, lipids, starch-glucose, and RNA-ribose. We describe the steps of sample preparation, MS analysis, and data handling required to obtain high-quality isotope labeling measurements that are applicable to MFA. By selecting target analytes that maximize identifiability of the key fluxes of interest, MS measurements of isotope labeling can provide a powerful platform for assessing metabolic fluxes in complex biochemical networks.

Library dependent LC-MS/MS acquisition via mzAPI/Live

The use of MS for characterization of small molecules, nucleotides, and proteins in model organisms as well as primary tissues and clinical samples continues to proliferate at a rapid pace. The complexity and dynamic range of target analytes in biological systems hinders comprehensive analysis and simultaneously drives improvements in instrument hardware and software. As a result, state-of-the-art commercial mass spectrometers are equipped with sophisticated embedded control systems that provide robust acquisition methods accessed through intuitive graphical interfaces. Although optimized for speed, these preconfigured scan functions are otherwise closed to end-user customization beyond simple, analytical-centric parameters supplied by the manufacturer. Here, we present an open-source framework (mzAPI/Live) that enables users to generate arbitrarily complex LC-MS(n) acquisition methods via simple Python scripting. As a powerful proof-of-concept, we demonstrate real-time assignment of tandem mass spectra through rapid query of NIST peptide libraries. This represents an unprecedented capability to make acquisition decisions based on knowledge of analyte structures determined during the run itself, thus providing a path toward biology-driven MS data acquisition for the broader community.

Biodegradation of three selected benzotriazoles in aquifer materials under aerobic and anaerobic conditions

We investigated the biodegradation of three selected benzotriazoles (BTs), namely benzotriazole (BT), 5-methyl-benzotriazole (5-TTri) and 5-chloro-benzotriazole (CBT), in aquifer materials. Biodegradation experiments were conducted in microcosms with fresh groundwater and aquifer sediment materials under aerobic and anaerobic (nitrate, sulfate, and Fe (III) reducing) conditions. All three BTs were degraded by microorganisms in aquifer materials under aerobic and anaerobic conditions. Under aerobic conditions, BT and 5-TTri were found to be degraded fastest with their half-lives of 43 days and 31 days, respectively, among the redox conditions used. Under anaerobic conditions, CBT was found to be degraded better with its half-life of 21 days under nitrate reducing conditions than under aerobic conditions with its half-life of 47 days. The two BT derivatives 5-TTri and CBT could be biotransformed into BT via demethylation and dechlorination reactions, respectively.

Spectral deconvolution for gas chromatography mass spectrometry-based metabolomics: current status and future perspectives

Mass spectrometry coupled to gas chromatography (GC-MS) has been widely applied in the field of metabolomics. Success of this application has benefited greatly from computational workflows that process the complex raw mass spectrometry data and extract the qualitative and quantitative information of metabolites. Among the computational algorithms within a workflow, deconvolution is critical since it reconstructs a pure mass spectrum for each component that the mass spectrometer observes. Based on the pure spectrum, the corresponding component can be eventually identified and quantified. Deconvolution is challenging due to the existence of co-elution. In this review, we focus on progress that has been made in the development of deconvolution algorithms and provide thoughts on future developments that will expand the application of GC-MS in metabolomics.

Review: mass spectrometry in Russia

The present review covers the main research in the area of mass spectrometry from the 1990s which was about the same time as the Russian Federation emerged from the collapse of the Soviet Union (USSR). It consists of two main parts-application of mass spectrometry to chemistry and related fields and creation and development of mass spectrometric technique. Both traditional and comparatively new mass spectrometric methods were used to solve various problems in organic chemistry (reactivity of gas-phase ions, structure elucidation and problems of identification, quantitative and trace analysis, differentiation of stereoisomers, derivatization approaches etc.), biochemistry (proteomics and peptidomics, lipidomics), medical chemistry (mainly the search of biomarkers, pharmacology, doping control), environmental, petrochemistry, polymer chemistry, inorganic and physical chemistry, determination of natural isotope ratio etc. Although a lot of talented mass spectrometrists left Russia and moved abroad after the collapse of the Soviet Union, the vitality of the mass spectral community proved to be rather high, which allowed the continuation of new developments in the field of mass spectrometric instrumentation. They are devoted to improvements in traditional magnetic sector mass spectrometers and the development of new ion source types, to analysis and modification of quadrupole, time-of-flight (ToF) and ion cyclotron resonance (ICR) analyzers. The most important achievements are due to the creation of multi-reflecting ToF mass analyzers. Special attention was paid to the construction of compact mass spectrometers, particularly for space exploration, of combined instruments, such as ion mobility spectrometer/mass spectrometer and accelerating mass spectrometers. The comparatively young Russian Mass Spectrometry Society is working hard to consolidate the mass spectrometrists from Russia and foreign countries, to train young professionals on new appliances and regularly holds conferences on mass spectrometry. For ten years, a special journal Mass-spektrometria has published papers on all disciplines of mass spectrometry.

Isotopically nonstationary 13C metabolic flux analysis

(13)C metabolic flux analysis (MFA) is a powerful approach for quantifying cell physiology based upon a combination of extracellular flux measurements and intracellular isotope labeling measurements. In this chapter, we present the method of isotopically nonstationary (13)C MFA (INST-MFA), which is applicable to systems that are at metabolic steady state, but are sampled during the transient period prior to achieving isotopic steady state following the introduction of a (13)C tracer. We describe protocols for performing the necessary isotope labeling experiments, for quenching and extraction of intracellular metabolites, for mass spectrometry (MS) analysis of metabolite labeling, and for computational flux estimation using INST-MFA. By combining several recently developed experimental and computational techniques, INST-MFA provides an important new platform for mapping carbon fluxes that is especially applicable to animal cell cultures, autotrophic organisms, industrial bioprocesses, high-throughput experiments, and other systems that are not amenable to steady-state (13)C MFA experiments.

Design and application of a data-independent precursor and product ion repository

The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.

Implicit biology in peptide spectral libraries

Mass spectral libraries are collections of mass spectra curated specifically to facilitate the identification of small molecules, metabolites, and short peptides. One of the most comprehensive peptide spectral libraries is curated by NIST and contains upward of half a million annotated spectra dominated by human and model organisms including budding yeast and mouse. While motivated primarily by the technological goal of increasing sensitivity and specificity in spectral identification, we have found that the NIST spectral library constitutes a surprisingly rich source of biological knowledge. In this Article, we show that data-mining of these published libraries while applying strict empirical thresholds yields many characteristics of protein biology. In particular, we demonstrate that the size and increasingly comprehensive nature of these libraries, generated from whole-proteome digests, enables inference from the presence but crucially also from the absence of spectra for individual peptides. We illustrate implicit biological trends that lead to significant absence of spectra accounted for by complex post-translational modifications and overlooked proteolytic sites. We conclude that many subtle biological signatures such as genetic variants, regulated proteolysis, and post-translational modifications are exposed through the systematic mining of spectral collections originally compiled as general-purpose, technology-oriented resources.

Biodegradation of the ultraviolet filter benzophenone-3 under different redox conditions

Biodegradation of the ultraviolet (UV) filter benzophenone-3 (BP-3) was investigated in the laboratory to understand its behavior and fate under oxic and anoxic (nitrate, sulfate, and Fe [III]-reducing) conditions. Biodegradation experiments were conducted in microcosms with 10% of activated sludge and digested sludge under oxic and anoxic conditions, respectively. Benzophenone-3 was well degraded by microorganisms under each redox condition. Under the redox conditions studied, the biodegradation half-life for BP-3 had the following order: oxic (10.7 d) > nitrate-reducing (8.7 d) > Fe (III)-reducing (5.1 d) > sulfate-reducing (4.3 d) ≥ anoxic unamended (4.2 d). The results suggest that anaerobic biodegradation is a more favorable attenuation mechanism for BP-3. Biodegradation of BP-3 produced two products, 4-cresol and 2,4-dihydroxybenzophenone, under oxic and anoxic conditions. Biotransformation of BP-3 to 2,4-dihydroxybenzophenone by way of demethylation of the methoxy substituent (O-demethylation) occurred in cultures under each redox condition. The further biotransformation of 2,4-dihydroxybenzophenone to 4-cresol was inhibited under oxic, nitrate-reducing, and sulfate-reducing conditions.

TagFinder: preprocessing software for the fingerprinting and the profiling of gas chromatography-mass spectrometry based metabolome analyses

GC-MS based metabolome studies aim for the complete identification and relative or absolute quantification of metabolites in complex extracts from a large diversity of biological materials. The resulting high-throughput chromatography data files are typically processed following two complementary workflows, namely, fingerprinting and profiling. For fingerprinting studies all observed mass features, here called mass spectral tags (MSTs), are quantified in a nontargeted and (within the limits of the GC-MS technology) comprehensive approach. Fingerprinting allows for the discovery of MSTs, which, in the sense of a biomarker, indicate significant changes of metabolite pool sizes. The significance and relevance of such MSTs are typically tested in comparison to standardized reference samples. Only after this confirmation step are the relevant MSTs identified and the underlying metabolic biomarkers elucidated. Both the metabolite fingerprinting and profiling approaches are essential to modern biotechnological investigations. Studies which are aimed at establishing the substantial equivalence at metabolic level or aim to breed for optimum quality of human food or animal feed especially benefit from the potential to discover novel unforeseen metabolic factors in fingerprinting approaches and from the option to demonstrate unchanged pool sizes of known metabolites in the metabolic profiling mode. As GC-MS technology represents one essential element which contributes to investigations of substantial equivalence, we have developed a dedicated software tool, the TagFinder chromatography data preprocessing suite, which has all essential functions to support both fundamental workflows of modern metabolomic studies. In this chapter, we describe the TagFinder software and its application to the assessment of metabolic phenotypes in fingerprinting and profiling analyses.

Concomitant hydride and proton transfer: an essay on competing and consecutive key reactions occurring in gaseousion/neutral complexes

The interplay of proton transfer and hydride transfer reactions in alkylbenzenium ions and related protonated di- and oligophenylalkanes is presented and discussed. While intra- and interannular proton exchange has been recognised to be an ubiquitous feature in protonated arenes, hydride abstraction is much less obvious but can become a dominating fragmentation channel in metastable ions of tert-butyl-substituted alkylbenzenium ions and related carbocations. In such cases, proton-induced release of the tert-butyl cation gives rise to ion/neutral complexes as reactive intermediates, for example, [(CH(3))(3)C(+)...arylCH(2)(α)(CH(2))(n)CH(2)(ω)aryl '] with n ≥ 0, and highly regioselective intra-complex hydride transfer occurs from all of the benzylic methylene hydride ion donor groups (α-CH(2) and ω-CH(2)) to the tert-butyl cation acting as a Lewis acid. Substituent effects on the individual contributions to the overall hydride transfer from different donor sites, including ortho-methyl groups, in particular, and the concomitant intra- complex proton transfer from the tert-butyl cation to the neutral diarylalkane constituent corroborate the view of "bisolvated" complexes as the central intermediates, in which the carbenium ion is coordinated to both of the aromatic π-electron systems. The role of cyclisation processes converting the benzylic, [M - H](+) type, ions into the isomeric benzenium, [M + H](+)-type, ions prior to fragmentation is demonstrated for several cases. This overall scenario, consisting of consecutive and/or competing intra-complex hydride abstraction and proton transfer, intraannular proton shifts (H+ ring walk) and interannular proton transfer, hydrogen exchange ("scrambling") processes, and cyclisation and other electrophilic substitution reactions, is of general importance in this field of gas-phase ion chemistry, and more recent examples concerning protonated ethers, benzylpyridinium and benzylammmonium ions are discussed in which these recurring features play central and concerted mechanistic roles as well.

Recent advances of metabolomics in plant biotechnology

Biotechnology, including genetic modification, is a very important approach to regulate the production of particular metabolites in plants to improve their adaptation to environmental stress, to improve food quality, and to increase crop yield. Unfortunately, these approaches do not necessarily lead to the expected results due to the highly complex mechanisms underlying metabolic regulation in plants. In this context, metabolomics plays a key role in plant molecular biotechnology, where plant cells are modified by the expression of engineered genes, because we can obtain information on the metabolic status of cells via a snapshot of their metabolome. Although metabolome analysis could be used to evaluate the effect of foreign genes and understand the metabolic state of cells, there is no single analytical method for metabolomics because of the wide range of chemicals synthesized in plants. Here, we describe the basic analytical advancements in plant metabolomics and bioinformatics and the application of metabolomics to the biological study of plants.

Determination of elemental composition of volatile organic compounds from Chinese rose oil by spectral accuracy and mass accuracy

Elemental composition determination of volatile organic compounds through high mass accuracy and isotope pattern matching could not be routinely achieved with a unit-mass resolution mass spectrometer until the recent development of the comprehensive instrument line-shape calibration technology. Through this unique technology, both m/z values and mass spectral peak shapes are calibrated simultaneously. Of fundamental importance is that calibrated mass spectra have symmetric and mathematically known peak shapes, which makes it possible to deconvolute overlapped monoisotopes and their (13)C-isotope peaks and achieve accurate mass measurements. The key experimental requirements for the measurements are to acquire true raw data in a profile or continuum mode with the acquisition threshold set to zero. A total of 13 ions from Chinese rose oil were analyzed with internal calibration. Most of the ions produced high mass accuracy of better than 5 mDa and high spectral accuracy of better than 99%. These results allow five tested ions to be identified with unique elemental compositions and the other eight ions to be determined as a top match from multiple candidates based on spectral accuracy. One of them, a coeluted component (Nerol) with m/z 154, could not be identified by conventional GC/MS (gas chromatography/mass spectrometry) and library search. Such effective determination for elemental compositions of the volatile organic compounds with a unit-mass resolution quadrupole system is obviously attributed to the significant improvement of mass accuracy. More importantly, high spectral accuracy available through the instrument line-shape calibration enables highly accurate isotope pattern recognition for unknown identification.

Biodegradation of three selected benzotriazoles under aerobic and anaerobic conditions

We examined the biodegradability of three benzotriazoles (benzotriazole: BT, 5-methylbenzotriazole: 5-TTri and 5-chlorobenzotriazole: CBT) under aerobic and anaerobic (nitrate, sulfate, and Fe (III) reducing) conditions. All three benzotriazoles were degraded by microorganisms under aerobic and anaerobic conditions. Both the biodegradation efficiency and biodegradation products were dependent on the predominant terminal electron-accepting condition. Among the redox conditions studied, the shortest biodegradation half lives for BT and 5-TTri were 114 days and 14 days, respectively, under aerobic condition. The shortest half-life for CBT was 26 days under Fe (III) reducing condition. The longest biodegradation half lives for BT and CBT were 315 days and 96 days, respectively, under sulfate reducing condition, while that of 5-TTri was 128 days under nitrate reducing condition. These results suggest that aerobic biodegradation is the dominant natural attenuation mechanism for BT and 5-TTri, while the most favorable process for CBT was anaerobic biodegradation. This study demonstrated that different predominant terminal electron-acceptors present in natural environment play a key role on the biodegradation of BT, 5-TTri and CBT, leading to specific biodegradability. This could have significant implications on in-situ biodegradation of the selected benzotriazoles in aerobic and anaerobic waters, soils and sediments.

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry

Gas chromatography–mass spectrometry (GC–MS) acquisitions routinely yield hundreds to thousands of Electron Ionization (EI) mass spectra. The chemical identification of these spectra typically involves a search protocol that seeks an exact match to a reference spectrum. Reference spectra are found in comprehensive libraries of small molecule EI spectra curated by commercial and public entities. We developed ARISTO (Automatic Reduction of Ion Spectra To Ontology), a webtool, which provides information regarding the general chemical nature of the compound underlying an input EI mass spectrum. Importantly, ARISTO can provide such annotation without necessitating an exact match to a specific compound. ARISTO provides assignments to a subset of the ChEBI (Chemical Entities of Biological Interest) dictionary, an ontology, which aims to cover biologically relevant small molecules. Our system takes as input a mass spectrum represented as a series of mass and intensity pairs; the system returns a graphical representation of the supported ontology as well as a detailed table of suggested annotations along with their associated statistical evidence. ARISTO is accessible at this URL: http://www.ionspectra.org/aristo. The system is free, open to all and does not require registration of any sort.

Databases on food phytochemicals and their health-promoting effects

Considerable information on the chemistry and biological properties of dietary phytochemicals has accumulated over the past three decades. The scattering of the data in tens of thousands publications and the diversity of experimental approaches and reporting formats all make the exploitation of this information very difficult. Some of the data have been collected and stored in electronic databases so that they can be automatically updated and retrieved. These databases will be particularly important in the evaluation of the effects on health of phytochemicals and in facilitating the exploitation of nutrigenomic data. The content of over 50 databases on chemical structures, spectra, metabolic pathways in plants, occurrence and concentrations in foods, metabolism in humans and animals, biological properties, and effects on health or surrogate markers of health is reviewed. Limits of these databases are emphasized, and needs and recommendations for future developments are underscored. More investments in the construction of databases on phytochemicals and their effects on health are clearly needed. They should greatly contribute to the success of future research in this field.

Mass spectrometry and informatics: distribution of molecules in the PubChem database and general requirements for mass accuracy in surface analysis

Mass spectrometry is a powerful tool for the analysis and identification of substances across a broad range of technologies from proteomics and metabolomics through to surface analysis methods used for nanotechnology. A major challenge has been the development of automated methods to identify substances from the mass spectra. Public chemical databases have grown over 2 orders of magnitude in size over the past few years and have become a powerful tool in informatics approaches for identification. We analyze the popular PubChem database in terms of the population of substances with mass when resolved with typical mass spectrometer mass accuracies. We also characterize the average molecule in terms of the mass excess from nominal mass and the modal mass. It is shown, in agreement with other studies, that for the identification of unknowns a mass accuracy of around 1 ppm is required together with additional filtering using isotope patterns. This information is an essential part of a framework being developed for experimental library-free interpretation of complex molecule spectra in secondary ion mass spectrometry.

Electron ionization mass spectra of alkylated sulfabenzamides

Mono-, di- and trialkyl derivatives of 'sulfabenzamide' (N-4-aminophenylsulfonylbenzamide) have been prepared and their electron ionization (EI) mass spectra examined. It is found that the fragmentation of N-alkylsulfabenzamides (alkyl = CH(3) to n-C(5)H(11)) proceeds via a very specific rearrangement process. The proposed mechanism involves an intermediate formation of distonic molecular ions, and the driving force for this process is the formation of stable N-alkylphenylcyanide cations [R-N(+)≡CC(6)H(5)]. The findings are confirmed by exact mass measurements, tandem mass spectrometry (MS/MS) experiments and deuterium labeling.

On the accuracy and limits of peptide fragmentation spectrum prediction

We estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (CID) of peptide ions. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). We further investigated the accuracy of current predictors of peptide fragmentation spectra and found that they are more accurate than the ad-hoc models generally used by search engines (e.g., SEQUEST) and, surprisingly, approaching the empirical upper limit set by the average across-experiment spectral reproducibility (especially for charge +1 and charge +2 precursor ions). These results provide evidence that, in terms of accuracy of modeling, predicted peptide fragmentation spectra provide a viable alternative to spectral libraries for peptide identification, with a higher coverage of peptides and lower storage requirements. Furthermore, using five data sets of proteome digests by two different proteases, we find that PeptideART (a data-driven machine learning approach) is generally more accurate than MassAnalyzer (an approach based on a kinetic model for peptide fragmentation) in predicting fragmentation spectra but that both models are significantly more accurate than the ad-hoc models.

Advances in structure elucidation of small molecules using mass spectrometry

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users.

Unique para-effect in electron ionization mass spectra of bis(perfluoroacyl) derivatives of bifunctional aminobenzenes

A new kind of 'para-effect' under electron ionization (EI) conditions has been discovered for a series of bis(perfluoroacyl) derivatives of o-, m- and p-phenylenediamines, -hydroxybenzeneamines and -mercaptobenzeneamines of a common structure RCOX-C(6)H(4)-NHCOR (X = NH, S, O; R = CF(3), C(2)F(5), C(3)F(7)). Only the para-isomers showed successive loss of a radical RCO* and a molecule RCN, leading to very intense peaks in the EI spectra. The composition and the origin of the [M-COR-NCR](+) ions were confirmed by exact mass measurements and linked scan experiments. The proposed mechanism of their formation takes into account likely para-quinoid structures of the precursor ions. A similar rearrangement has not been observed for para-isomers in the series of bis(perfluoroacyl) derivatives of benzenediols, mercaptophenols and dimercaptobenzenes.

Influence of the input system (conventional versus organic farming) on metabolite profiles of maize ( Zea mays ) kernels

Maize ( Zea mays ) kernels grown conventionally and organically, respectively, were investigated using a gas chromatography/mass spectrometry (GC/MS)-based metabolite profiling methodology. By analysis of three cultivars grown at two locations with different input systems and at a third location where both organic and conventional farming were applied, the impact of the growing regime on the metabolite spectrum should be put into the context of natural variability. The applied analytical approach involved consecutive extraction of freeze-dried maize flour and subsequent subfractionation. Approximately 300 compounds from a broad spectrum of chemical classes were detected, of which 167 were identified. The metabolite profiling data were statistically assessed via principal component analysis (PCA) and analysis of variance (ANOVA). The PCA demonstrated that the observed separations were mainly due to genetic differences (cultivars) and environmental influences. The different input systems (conventional/organic) only led to minor differentiations. ANOVA and quantification of selected constituents confirmed these observations. Only three metabolites (malic acid, myo-inositol, and phosphate) were consistently different because of the employed input system if samples from all field trials were considered.

Proteomics data repositories

The field of proteomics, particularly the application of MS analysis to protein samples, is well established and growing rapidly. Proteomic studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and results accessible to proteomic researchers and biologists alike. This review of proteomics data repositories focuses exclusively on freely available, centralized data resources that disseminate or store experimental MS data and results. The resources chosen reflect a current "snapshot" of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers. Resources are described in terms of their intended purpose and the features and functionality provided to users.

A method for assessing and maintaining the reproducibility of mass spectrometric analyses of complex samples

Direct injection mass spectrometric analysis of biological samples is potentially an attractive approach to the discovery of diagnostic patterns for specific pathophysiological conditions because of its speed and simplicity. Despite the possible benefits offered by such a method, its extensive application has been limited so far by several factors, including the inadequate reproducibility of the analytical results. We describe a method for monitoring and optimizing the performance of mass spectrometers used for biomarker discovery studies, based on the analysis of patterns of standardized spectral features. The method was successfully applied to maintaining spectral reproducibility during a multi-day analysis of hundreds of serum samples despite an ion source failure, which necessitated minor maintenance. The monitoring method allowed the early detection of that failure and the restoration of the spectral profiles after the system was restarted.

Exploring human metabolites using the human metabolome database

The Human Metabolome Database (HMDB) is a Web-based bioinformatic/cheminformatic resource with detailed information about human metabolites and metabolic enzymes. It can be used for fields of study including metabolomics, biochemistry, clinical chemistry, biomarker discovery, medicine, nutrition, and general education. In addition to its comprehensive literature-derived data, the HMDB contains an extensive collection of experimental metabolite concentration data for plasma, urine, CSF, and/or other biofluids The HMDB is fully searchable, with many tools for viewing, sorting and extracting metabolite names, chemical structures, biofluid concentrations, enzymes, genes, NMR or MS spectra, and disease information. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, chemical structure information, physico-chemical data, reference NMR and MS spectra, normal and abnormal biofluid concentrations, tissue locations, disease associations, pathway information, enzyme data, gene sequence data, and SNP and mutation data, as well as extensive links to images, references and other public databases.

A method for monitoring and controlling reproducibility of intensity data in complex electrospray mass spectra: a thermometer ion-based strategy

Reproducibility in mass spectral data is important in both biomarker discovery and spectral database searching. We report a strategy, employing a series of substituted benzylpyridinium thermometer ions that can be used to monitor changes in performance of multiple aspects of an electrospray ionization source that impact the intensity axis of a spectrum. Performance attributes, which could confound even isotope-based quantification strategies, are readily assessed using a mixture of thermometer ions. Based on the observed behavior of the ions, a procedure is proposed for monitoring instrument performance and compensating for factors that affect reproducibility across both time and instruments.

Building consensus spectral libraries for peptide identification in proteomics

Spectral searching has drawn increasing interest as an alternative to sequence-database searching in proteomics. We developed and validated an open-source software toolkit, SpectraST, to enable proteomics researchers to build spectral libraries and to integrate this promising approach in their data-analysis pipeline. It allows individual researchers to condense raw data into spectral libraries, summarizing information about observed proteomes into a concise and retrievable format for future data analyses.

Retention index thresholds for compound matching in GC-MS metabolite profiling

The generation of retention index (RI) libraries is an expensive and time-consuming effort. Procedures for the transfer of RI properties between chromatography variants are, therefore, highly relevant for a shared use. The precision of RI determination and accuracy of RI transfer between 8 method variants employing 5%-phenyl-95%-dimethylpolysiloxane capillary columns was investigated using a series of 9 n-alkanes (C(10)-C(36)). The precision of the RI determination of 13 exemplary fatty acid methyl esters (C(8) ME-C(30) ME) was 0.22-0.33 standard deviation (S.D.) expressed in RI units in low complexity samples. In the presence of complex biological matrices this precision may deteriorate to 0.75-1.11. Application of the previously proposed Kováts, van den Dool or 3rd-5th order polynomial regression algorithms resulted in similar precision of RI calculation. For transfer of empirical van den Dool-RI properties between the chromatography variants 3rd order regression was found to represent the minimal necessary assumption. The range of typical regression coefficients was r(2)=0.9988-0.9998 and accuracy of RI prediction between chromatography variants varied between 5.1 and 19.8 (0.29-0.69%) S.D. of residual RI error, RI(predicted)-RI(determined) (n>64). Accuracy of prediction was enhanced when subsets of chemically similar compound classes were used for regression, for example organic acids and sugars exhibited 0.78 (n=29) and 3.74 (n=37) S.D. of residual RI error, respectively. In conclusion, we suggest use of percent RI error rather than absolute RI units for the definition of matching thresholds. Thresholds of 0.5-1.0% may apply to most transfers between chromatography variants. These thresholds will not solve all matching ambiguities in complex samples. Therefore, we recommend co-analysis of reference substances with each GC-MS profiling experiment. Composition of these defined reference mixtures may best approximate or mimic the quantitative and qualitative composition of the biological matrix under investigation.

A metabolomics based approach to assessing the toxicity of the polyaromatic hydrocarbon pyrene to the earthworm Lumbricus rubellus

The biochemical response of the earthworm Lumbricus rubellus to pyrene exposure was assessed using 1H nuclear magnetic resonance (NMR) spectroscopy, gas chromatography mass spectrometry (GC-MS) and pattern recognition techniques. Both analytical methods enabled the establishment of reproducible metabolic profiles. NMR analysis identified a total of 32 metabolites while GC-MS identified 51. The results demonstrate that not only is pyrene toxic to L. rubellus, but that alterations in its normal metabolic profile could be observed even when individuals were exposed to concentrations of 40mg kg(-1): a pollution level that is both below the concentration previously found to significantly reduce reproduction and within the range of polycyclic aromatic hydrocarbons (PAHs) found on some contaminated sites. Pyrene was found to cause a dose dependant decrease in lactate and the concentrations of the saturated fatty acids tetradecanoic, hexadecanoic and octadecanoic acid and an increase in production of the amino acids alanine, leucine, valine, isoleucine, lysine, tyrosine and methionine. It is proposed that this indicates impaired glucose metabolism, with an associated increase in fatty acid metabolism and changes in TCA cycle intermediates. This study demonstrates the versatility of metabolomics as a tool to monitor toxicity in the environment as opposed to utilising model species studied in a laboratory setting. Since it is a non-carcinogenic PAH, we propose that the metabolic changes observed in worms may reflect the non-specific toxic effects of pyrene as a typical, non-polar organic compound.

TagFinder for the quantitative analysis of gas chromatography--mass spectrometry (GC-MS)-based metabolite profiling experiments

MOTIVATION

Typical GC-MS-based metabolite profiling experiments may comprise hundreds of chromatogram files, which each contain up to 1000 mass spectral tags (MSTs). MSTs are the characteristic patterns of approximately 25-250 fragment ions and respective isotopomers, which are generated after gas chromatography (GC) by electron impact ionization (EI) of the separated chemical molecules. These fragment ions are subsequently detected by time-of-flight (TOF) mass spectrometry (MS). MSTs of profiling experiments are typically reported as a list of ions, which are characterized by mass, chromatographic retention index (RI) or retention time (RT), and arbitrary abundance. The first two parameters allow the identification, the later the quantification of the represented chemical compounds. Many software tools have been reported for the pre-processing, the so-called curve resolution and deconvolution, of GC-(EI-TOF)-MS files. Pre-processing tools generate numerical data matrices, which contain all aligned MSTs and samples of an experiment. This process, however, is error prone mainly due to (i) the imprecise RI or RT alignment of MSTs and (ii) the high complexity of biological samples. This complexity causes co-elution of compounds and as a consequence non-selective, in other words impure MSTs. The selection and validation of optimal fragment ions for the specific and selective quantification of simultaneously eluting compounds is, therefore, mandatory. Currently validation is performed in most laboratories under human supervision. So far no software tool supports the non-targeted and user-independent quality assessment of the data matrices prior to statistical analysis. TagFinder may fill this gap.

STRATEGY

TagFinder facilitates the analysis of all fragment ions, which are observed in GC-(EI-TOF)-MS profiling experiments. The non-targeted approach allows the discovery of novel and unexpected compounds. In addition, mass isotopomer resolution is maintained by TagFinder processing. This feature is essential for metabolic flux analyses and highly useful, but not required for metabolite profiling. Whenever possible, TagFinder gives precedence to chemical means of standardization, for example, the use of internal reference compounds for retention time calibration or quantitative standardization. In addition, external standardization is supported for both compound identification and calibration. The workflow of TagFinder comprises, (i) the import of fragment ion data, namely mass, time and arbitrary abundance (intensity), from a chromatography file interchange format or from peak lists provided by other chromatogram pre-processing software, (ii) the annotation of sample information and grouping of samples into classes, (iii) the RI calculation, (iv) the binning of observed fragment ions of equal mass from different chromatograms into RI windows, (v) the combination of these bins, so-called mass tags, into time groups of co-eluting fragment ions, (vi) the test of time groups for intensity correlated mass tags, (vii) the data matrix generation and (viii) the extraction of selective mass tags supported by compound identification. Thus, TagFinder supports both non-targeted fingerprinting analyses and metabolite targeted profiling.

AVAILABILITY

Exemplary TagFinder workspaces and test data sets are made available upon request to the contact authors. TagFinder is made freely available for academic use from http://www-en.mpimp-golm.mpg.de/03-research/researchGroups/01-dept1/Root_Metabolism/smp/TagFinder/index.html.

The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery

The future utility of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discover will be discussed, beginning with a brief description of the evolution of metabolomics and the utilization of the three most popular analytical platforms in such studies: NMR, GC-MS, and LC-MS. Emphasis is placed on recent developments in high-efficiency LC separations, sensitive electrospray ionization approaches, and the benefits to incorporating both in LC-MS-based approaches. The advantages and disadvantages of various quantitative approaches are reviewed, followed by the current LC-MS-based tools available for candidate biomarker characterization and identification. Finally, a brief prediction on the future path of LC-MS-based methods in metabolic profiling and metabolomic studies is given.

Development and validation of a spectral library searching method for peptide identification from MS/MS

A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time-consuming and error-prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open-source, functionally complete, high-throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high-quality spectral library was constructed by combining the high-confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30,000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.