On-line acquisition, analysis, and e-mailing of high-resolution exact-mass electron impact/chemical ionization mass spectrometry data acquired using an automated direct probe

A complete automation package has been developed for data acquisition, processing, interpreting, and e-mailing of high-resolution exact-mass electron impact (EI) and chemical ionization (CI) mass spectrometry data. A commercial high performance magnetic sector mass spectrometer equipped with a commercial programmable robotic direct probe was used. The software package contains a series of modules that automatically performs all the functions necessary for data reduction and reporting. In sequential order, these functions include downloading of sample information from a corporate database, creation of a sample list, acquisition of high-resolution exact-mass data, processing of the data, generation of an exact-mass report, e-mailing of the results to the requesting chemists, and finally shutting down of the instrument. The performance of the system was evaluated with nearly 500 samples. The system was found to be reliable and robust with a small average systematic mass error of −0.47 mmu and a standard deviation of 1.61 mmu.     

Software tool for mining liquid chromatography/multi‐stage mass spectrometry data for comprehensive glycerophospholipid profiling

Electrospray ionization mass spectrometry (ESI‐MS) has emerged as an indispensable tool in the field of lipidomics. Despite the growing interest in lipid analysis, there are only a few software tools available for data evaluation, as compared for example to proteomics applications. This makes comprehensive lipid analysis a complex challenge. Thus, a computational tool for harnessing the raw data from liquid chromatography/mass spectrometry (LC/MS) experiments was developed in this study and is available from the authors on request. The Profiler‐Merger‐Viewer tool is a software package for automatic processing of raw‐data from data‐dependent experiments, measured by high‐performance liquid chromatography hyphenated to electrospray ionization hybrid linear ion trap Fourier transform mass spectrometry (FTICR‐MS and Orbitrap) in single and multi‐stage mode. The software contains three parts: processing of the raw data by Profiler for lipid identification, summarizing of replicate measurements by Merger and visualization of all relevant data (chromatograms as well as mass spectra) for validation of the results by Viewer. The tool is easily accessible, since it is implemented in Java and uses Microsoft Excel (XLS) as output format. The motivation was to develop a tool which supports and accelerates the manual data evaluation (identification and relative quantification) significantly but does not make a complete data analysis within a black‐box system. The software's mode of operation, usage and options will be demonstrated on the basis of a lipid extract of baker's yeast (S. cerevisiae). In this study, we focused on three important representatives of lipids: glycerophospholipids, lyso‐glycerophospholipids and free fatty acids. Copyright © 2010 John Wiley & Sons, Ltd.     

Modern MALDI time‐of‐flight mass spectrometry

This paper focuses on development of time‐of‐flight (TOF) mass spectrometry in response to the invention of matrix‐assisted laser desorption/ionization (MALDI). Before this breakthrough ionization technique for nonvolatile molecules, TOF was generally considered as a useful tool for exotic studies of ion properties but was not widely applied to analytical problems. Improved TOF instruments and software that allow the full potential power of MALDI to be applied to difficult biological applications are described. A theoretical approach to the design and optimization of MALDI‐TOF instruments for particular applications is presented. Experimental data are provided that are in excellent agreement with theoretical predictions of resolving power and mass accuracy. Data on sensitivity and dynamic range using kilohertz laser rates are also summarized. These results indicate that combinations of high‐performance MALDI‐TOF and TOF‐TOF with off‐line high‐capacity separations may ultimately provide throughput and dynamic range several orders of magnitude greater than those currently available with electrospray LC‐MS and MS‐MS. Copyright © 2009 John Wiley & Sons, Ltd.     

Mirion—A Software Package for Automatic Processing of Mass Spectrometric Images

Mass spectrometric imaging (MSI) techniques are of growing interest for the Life Sciences. In recent years, the development of new instruments employing ion sources that are tailored for spatial scanning allowed the acquisition of large data sets. A subsequent data processing, however, is still a bottleneck in the analytical process, as a manual data interpretation is impossible within a reasonable time frame. The transformation of mass spectrometric data into spatial distribution images of detected compounds turned out to be the most appropriate method to visualize the results of such scans, as humans are able to interpret images faster and easier than plain numbers. Image generation, thus, is a time-consuming and complex yet very efficient task. The free software package “Mirion,” presented in this paper, allows the handling and analysis of data sets acquired by mass spectrometry imaging. Mirion can be used for image processing of MSI data obtained from many different sources, as it uses the HUPO-PSI-based standard data format imzML, which is implemented in the proprietary software of most of the mass spectrometer companies. Different graphical representations of the recorded data are available. Furthermore, automatic calculation and overlay of mass spectrometric images promotes direct comparison of different analytes for data evaluation. The program also includes tools for image processing and image analysis.

Ethylene Glycol Electrooxidation Based on Pentangle‐Like PtCu Nanocatalysts

The research of active and stable electrocatalysts toward liquid‐fuel oxidation reaction is of great significance for the large‐scale commercialization of fuel cells. Although extensive efforts have been devoted to pursuing high‐performance nanocatalysts for fuel cells, both the high cost and sluggish reaction kinetics have been two major drawbacks that limited its commercial development. In this regard, we demonstrated a facile solvothermal method for the syntheses of an advanced class of PtCu nanocatalysts with a unique pentangle‐like shape. By combining the merits of a highly active surface area as well as the synergistic and electronic effects, the as‐prepared pentangle‐like Pt₃Cu nanocatalysts showed superior electrocatalytic activity towards ethylene glycol oxidation with a mass and specific activities of 5162.6 mA mg^?1 and 9.7 mA cm^?2, approximately 5.0 and 5.1 times higher than the commercial Pt/C, respectively. More significantly, the Pt₃Cu pentangle also showed excellent long‐term stability with less activity decay and negligible changes in structure after 500 cycles, indicating another class of anode catalysts for fuel cells and beyond.     

Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-resolution exact-mass electrospray ionization mass spectral data

A system has been designed to automatically acquire high-resolution (>50,000 FWHM), exact-mass (mass measurement error ≤3 mmu) electrospray ionization mass spectra with a commercial Fourier transform ion cyclotron resonance mass spectrometer equipped with a high-field (9.4 tesla) superconducting magnet and a commercial autosampler. Upon the injection of each individual sample, the autosampler transmits a contact closure signal to the previously tuned and calibrated mass spectrometer to initiate data acquisition. A software package was designed to run off-line and to accept a sample list with input information for each of the samples. Then for each of the samples, the software automatically processes the acquired data, interprets the exact-mass data by correlating the observed masses with predicted masses computed from proposed elemental formulas, and then finally prints the spectra, peak lists, and exact-mass reports, and e-mails the exact-mass reports to the submitting chemists. With this automation package, large numbers of samples can be run unattended while obtaining exact masses for all the abundant ions in the spectra. Sample turnaround times are reduced with a corresponding increase in sample throughput. The performance of the system was evaluated with nearly 700 samples with a precalibrated instrument, without the presence of an internal standard. The system was found to be reliable and robust with a fitted standard deviation of 0.32 mmu and a small average systematic mass error of ?0.28 mmu. Typical data acquired with the system have resolving powers >50,000 (FWHM) and mass errors <1.0 mmu.     

Static TOF‐SIMS. A VAMAS interlaboratory study. Part II — accuracy of the mass scale and G‐SIMS compatibility

An interlaboratory study involving 32 time‐of‐flight static SIMS instruments from 13 countries has been conducted. In Part I of the analysis of data, we showed that 84% of instruments have excellent repeatabilities of better than 1.9% and that a relative instrument spectral response (RISR) can be used to evaluate variations between different generic types of instrument. Use of the RISR improves comparability between instruments by a factor of 33. Here, in Part II, we study the accuracy of the mass scale calibration in TOF‐SIMS and evaluate instrument compatibility with G‐SIMS. We show that the accuracy of calibration of the mass scale is much poorer than generally expected (?60 ppm for peaks <200 u and ?150 ppm for a large molecular peak at 647 u). This is a major issue for analysts. Elsewhere, we have developed a detailed study of the factors affecting the mass calibration and have developed a generic protocol that improves accuracy by a factor of 5. Here, this framework of understanding is used to interpret the results presented. Furthermore, we show that eight out of the ten participants submitting data for G‐SIMS could use operating conditions that generated G‐SIMS spectra of the PC reference material. This demonstrates that G‐SIMS may be conducted with a wide variety of instrument designs. © Crown Copyright 2007. Reproduced by permission of the Controller of HMSO. Published by John Wiley & Sons, Ltd.     

Static TOF‐SIMS — a VAMAS interlaboratory study. Part I. Repeatability and reproducibility of spectra

An interlaboratory study involving 32 Time‐of‐Flight Static SIMS instruments from 12 countries has been conducted. Analysts were supplied, by NPL, with a protocol for analysis together with three reference materials; a thin layer of polycarbonate (PC) on a silicon wafer, a thin layer of polystyrene (PS) oligomers on etched silver and poly(tetrafluoroethylene) (PTFE). The study involved static SIMS analysis of each reference material for both positive and negative polarity secondary ions. The option to test instrument suitability for G‐SIMS was also provided. The results of this study show that over 84% of instruments have excellent repeatabilities of better than 1.9%. Repeatabilities can be as good as 0.4%. A relative instrument spectral response (RISR) is calculated for each instrument for each reference material and ion polarity. The RISR is used to evaluate variations in spectral response between different generic types of SIMS instruments. Use of the RISR allows the identification of contamination, charge stabilisation problems and incorrectly functioning ion detectors. The high quality of the data presented here allows the RISR to reveal differences in individual operation of each instrument such as the use of apertures to remove metastables from the spectra and the use of different post‐acceleration voltages for ion detection. Spectral reproducibility can be measured, here, by the equivalence of RISRs between materials and ion polarities. It is found that reproducibilities are on average 10% but can be as good as 4% for the best instruments. This figure shows the consistency between instruments in measuring spectra from different samples. This study sets out the basic framework to develop static secondary ion mass spectrometry (SSIMS) as a reliable measurement method. © Crown Copyright 2005. Reproduced with the permission of Her Majestry's Stationery Office. Published by John Wiley & Sons, Ltd.     

Critical evaluation of screening techniques for emerging environmental contaminants based on accurate mass measurements with time‐of‐flight mass spectrometry

Emerging contaminants from wastewater effluent samples were analysed, using posttarget and nontarget analysis techniques. The samples were analysed with an ultra performance liquid chromatograph‐time‐of‐flight mass spectrometer (UPLC‐TOF‐MS), and the resulting data were processed with commercial deconvolution software. The method works well for posttarget analysis with prior information about the retention times of the compounds of interest. With positive polarity, 63 of 66 compounds and with negative polarity, 18 of 20 compounds were correctly identified in a spiked sample, while two compounds of a total of 88 fell out of the mass range. Furthermore, a four‐stage process for identification was developed for the posttarget analysis lacking the retention time data. In the process, the number of candidate compounds was reduced by using the accurate mass of selected compounds in two steps (stages 1 and 2), structure–property relationships (stage 3) and isotope patterns of the analytes (stage 4). The process developed was validated by analysing wastewater samples spiked with 88 compounds. This procedure can be used to gain a preliminary indication of the presence of certain analytes in the samples. Nontarget analysis was tested by applying a theoretical mass spectra library for a wastewater sample spiked with six pharmaceuticals. The results showed a high number of false identifications. In addition, manual processing of the data was considered laborious and ineffective. Finally, the posttarget analysis was applied to a real wastewater sample. The analysis revealed the presence of six compounds that were afterwards confirmed with standard compounds as being correct. Three psycholeptics (nordiazepam, oxazepam and temazepam) could be tentatively identified, using the identification process developed. Posttarget analysis with UPLC‐TOF‐MS proved to be a promising method for analysing wastewater samples, while we concluded that the software for nontarget analysis will need improvement before it can be used in environmental analytical work with LC‐TOF‐MS systems. Copyright © 2012 John Wiley & Sons, Ltd.     

Comparison of electron ionization mass spectra of some organic compounds (MW < 200 Da) recorded on mass spectrometers of various types

Low-resolution electron ionization mass spectra recorded on various types of mass spectrometers (time-of-flight, quadrupole, and three-dimensional ion trap) were compared. A model mixture of 10 organic compounds (MW < 200 Da) was analyzed by gas chromatography-mass spectrometry. Pure mass spectra of analytes were extracted using the AMDIS software. The best repeatability was achieved for the time-of-flight mass spectrometer. The mass spectra recorded by a quadrupole and a time-of-flight mass spectrometer were quite similar. In the case of these instruments, library search using a commercial mass spectral data base (NIST’05) gave satisfactory result for each analyte (rank 1 or 2 in the “hit list”; Match > 900). In some cases, the mass spectra of model compounds recorded by the ion trap mass spectrometer differed in intensity of certain mass spectral peaks (but not in the set of peaks) from the mass spectra presented in the library and from the experimental mass spectra recorded by the time-of-flight and quadrupole instruments.     

Nitrogen‐Doped Graphitic Porous Carbon Nanosheets Derived from In Situ Formed g‐C3N4 Templates for the Oxygen Reduction Reaction

Heteroatom‐doped carbon materials have been considered as potential substitutes for Pt‐based electrocatalysts for the oxygen reduction reaction (ORR) in alkaline fuel cells. Here we report the synthesis of oxygen‐containing nitrogen‐doped carbon (ONC) nanosheets through the carbonization of a mixture that contained glucose and dicyandiamide (DCDA). In situ formed graphitic carbon nitride (g‐C₃N₄) derived from DCDA provided a nitrogen‐rich template, thereby facilitating the formation of ONC nanosheets. The resultant ONC materials with high nitrogen content, high specific surface areas, and highly mesoporous total volume displayed excellent electrochemical performance, including a similar ORR onset potential, half‐potential, a higher diffusion‐limited current, and excellent tolerance to methanol than that of the commercial Pt/C catalyst, respectively. Moreover, the ONC‐850 nanosheet displayed high long‐term durability even after 1000 cycles as well as a high electron transfer number of 3.92 (4.0 for Pt/C). Additionally, this work provides deeper insight into these materials and a versatile strategy for the synthesis of cost‐effective 2D N‐doped carbon electrocatalysts.     

An efficient and extensible format,library, and API for binary trajectory data from molecular simulations

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high‐performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost‐efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present “Trajectory Next Generation” (TNG)—a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state‐of‐the‐art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. © 2013 Wiley Periodicals, Inc.     

Chemical cross‐linking with NHS esters: a systematic study on amino acid reactivities

Structure elucidation of tertiary or quaternary protein structures by chemical cross‐linking and mass spectrometry (MS) has recently gained importance. To locate the cross‐linker modification, dedicated software is applied to analyze the mass or tandem mass spectra (MS/MS). Such software requires information on target amino acids to limit the data analysis time. The most commonly used homobifunctional N‐hydroxy succinimide (NHS) esters are often described as reactive exclusively towards primary amines, although side reactions with tyrosine and serine have been reported. Our goal was to systematically study the reactivity of NHS esters and derive some general rules for their attack of nucleophilic amino acid side chains in peptides. We therefore studied the cross‐linking reactions of synthesized and commercial model peptides with disuccinimidyl suberate (DSS). The first reaction site in all cases was expectedly the α‐NH₂‐group of the N‐terminus or the ε‐NH₂‐group of lysine. As soon as additional cross‐linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type‐1 cross‐link formation. The reactivity is highly dependent on the pH and on adjacent amino acids. Copyright © 2009 John Wiley & Sons, Ltd.     

Commercial formaldehyde standard for mass calibration in mass spectrometry

Common calibration standards for mass spectrometry can be a source of many problems including instrument contamination, ionization suppression and formation of unidentified ions during subsequent analysis. In this article, we present a new approach for the calibration of mass analyzers such as a quadrupole–time‐of‐flight mass spectrometry using a diluted solution of commercial formaldehyde. Formaldehyde is an inexpensive and commonly used solvent, and its intrinsic polymerization leads to the formation of polyoxymethylene (POM) oligomers, which are excellent multiple calibration standards for a low‐mass spectral region (up to m/z 400) in the positive and negative mode of electrospray ionization. We explore the nature and origin of these polymeric species and attributed them to chemical reactions of formaldehyde and stabilizing agents in commercial formaldehyde solutions and during electrospray ionization. In contrast to other calibrants, POM oligomers do not contaminate the instrument and can easily be removed from the sample delivery system. Using tandem mass spectrometry, we elucidate the structures of the detected POM oligomers and report their reference masses, which are tightly spaced by 30 mass units. In our calibration method, mass errors of <5 ppm can be obtained from m/z 20–400 using external calibration with a simple one‐point zero‐order correction of spectral data and without the need for operation of a dual spray or internal calibrants. Our approach will be particularly useful for those interested in the analysis of fragile ions with low m/z values and can function at instrumental conditions required for analysis of the most labile metabolites and environmental contaminants. Copyright © 2015 John Wiley & Sons, Ltd.     

Combining targeted and nontargeted data analysis for liquid chromatography/high‐resolution mass spectrometric analyses

Increasing importation of food and the diversity of potential contaminants have necessitated more analytical testing of these foods. Historically, mass spectrometric methods for testing foods were confined to monitoring selected ions (SIM or MRM), achieving sensitivity by focusing on targeted ion signals. A limiting factor in this approach is that any contaminants not included on the target list are not typically identified and retrospective data mining is limited. A potential solution is to utilize high‐resolution MS to acquire accurate mass full‐scan data. Based on the instrumental resolution, these data can be correlated to the actual mass of a contaminant, which would allow for identification of both target compounds and compounds that are not on a target list (nontargets). The focus of this research was to develop software algorithms to provide rapid and accurate data processing of LC/MS data to identify both targeted and nontargeted analytes. Software from a commercial vendor was developed to process LC/MS data and the results were compared to an alternate, vendor‐supplied solution. The commercial software performed well and demonstrated the potential for a fully automated processing solution.     

Automated data massaging, interpretation, and e-mailing modules for high throughput open access mass spectrometry

Hardware components and software modules were configured to enhance the automation, efficiency, and reliability of a commercial open access atmospheric pressure ionization mass spectrometry (API/MS) system for flow injection analysis. The data massaging module is a versatile package for data manipulation/reduction which is initialized upon detecting the end of data acquisition and can function in parallel during the data acquisition of the next sample. The data interpretation module compares the ions in the acquired mass spectrum with the predicted molecular adduct ions in different charge states, as well as the predicted isotopic distributions, possible artifact, polymer/cluster, byproduct/fragmentation ions, and then uses the results to score the quality of the spectrum. The e-mailing module transmits the spectrum and interpretation report to the desktop computer of the submitting chemist where the spectrum can be displayed and the report viewed. A scheme is also presented for the automated interpretation of an API mass spectrum for the determination of the most likely molecular weights of the components present in an “unknown” sample. Related flow diagrams, algorithms, and applications are illustrated.     

Interfaces for data processing in surface analysis

As computer controlled instruments for surface analysis are in common use for many years, the problem of exchangeability of analytical data has attracted interest in the surface analysis community. More and more examples for the development of standarized data formats as the VAMAS format [1] and the Standard for Chromatography Data Communication from the AIA [2] have been published. There are a few attempts to establish standardized “data dictionaries” e.g. the parameter lists describing AES and XPS spectra pusblished in Surface Science Spectra [3, 4]. If several different analysis methods (such as AES, SAM, XPS, SIMS, STM, AFM, EPMA, …) are applied to the same sample, a quite independent and open approach is needed to be able to combine data of various instruments in a common data evaluation procedure. It could be the basic concept of real mutli-method analysis. The public domain software package MAXMIND has been developed, as only a standardized data exchange and storage format based on data dictionaries can guarantee a high level of independence of proprietary measurement systems. Received: 16 January 1997 / Revised: 9 May 1997 / Accepted: 14 May 1997     

Interfaces for data processing in surface analysis

As computer controlled instruments for surface analysis are in common use for many years, the problem of exchangeability of analytical data has attracted interest in the surface analysis community. More and more examples for the development of standarized data formats as the VAMAS format [1] and the Standard for Chromatography Data Communication from the AIA [2] have been published. There are a few attempts to establish standardized “data dictionaries” e.g. the parameter lists describing AES and XPS spectra pusblished in Surface Science Spectra [3, 4]. If several different analysis methods (such as AES, SAM, XPS, SIMS, STM, AFM, EPMA, …) are applied to the same sample, a quite independent and open approach is needed to be able to combine data of various instruments in a common data evaluation procedure. It could be the basic concept of real mutli-method analysis. The public domain software package MAXMIND has been developed, as only a standardized data exchange and storage format based on data dictionaries can guarantee a high level of independence of proprietary measurement systems. Received: 16 January 1997 / Revised: 9 May 1997 / Accepted: 14 May 1997