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.     

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.     

MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization

The rapid advancements in mass spectrometry (MS) instrumentation, particularly in Fourier transform (FT) MS, have made the acquisition of high-resolution and high-accuracy mass measurements routine. However, the software tools for the interpretation of high-resolution MS data are underdeveloped. Although several algorithms for the automatic processing of high-resolution MS data are available, there is still an urgent need for a user-friendly interface with functions that allow users to visualize and validate the computational output. Therefore, we have developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution MS data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution MS data, and manually validate automatically processed results. Furthermore, it provides easy, fast, and reliable interpretation of top-down, middle-down, and bottom-up MS data. MASH Suite is convenient, easily operated, and freely available. It can greatly facilitate the comprehensive interpretation and validation of high-resolution MS data with high accuracy and reliability.

Increasing high‐throughput Discovery bioanalysis using automated selected reaction monitoring compound optimization,ultra‐high‐pressure liquid chromatography,and single‐step sample preparation workflows

QuickQuan is an integrated software package for Thermo Scientific triple quadrupole mass spectrometers that allows users to automate routine operations ranging from method development to data processing. QuickQuan automated optimization of compound‐selected reaction monitoring (SRM) transitions by evaluating both positive and negative polarities during an infusion. Whichever mode produces the most intense Q1 scan is then carried to product ion spectra. QuickQuan then writes these SRM methods to a shared network database. The total volume of compound needed is 100 µL infused over approximately 1.6 min. The auto‐optimization is carried out in 96‐well plates and does not require an operator present. The SRM database was shared between two identical TSQ Quantum mass spectrometers. For data acquisition, QuickQuan automatically created a sequence file complete with a data processing method pre‐populated with compound IDs and corresponding SRM transitions. To increase throughput we coupled each Finnigan Quantum with ultra‐high‐pressure liquid chromatography (uHPLC) accomplished using 4× Ultra Flux quaternary pumps that were designed to handle pressures up to 15 000 psi. The total run time for all analyses was 1.2 min using BEH 1.7 µm particle C18 columns. Further time reductions were realized with sample preparation accomplished using Strata Impact protein precipitation plates which provided an in‐well protein crash and 0.20 micron filtering in a one‐step process. Pharmacokinetic data turnaround time was significantly improved by combining these three techniques of automated method development with the speed efficiency of uHPLC and a single step in well sample preparation. Copyright © 2009 John Wiley & Sons, Ltd.     

Electronic data acquisition and operational control system for time-of-flight sputtered neutral mass spectrometer

A new electric data acquisition and operational control system was developed for time-of-flight sputtered neutral mass spectrometry (TOF-SNMS). The system is designed for high-speed data acquisition, data processing, and data streaming. The developed system is constructed on an NI-PXI platform and provides timing clocks for the TOF-SNMS operation. The system performs data processing of noise suppression and ion counting while acquiring TOF mass spectrum for 13-microsecond length at sampling rate of 3 GS/s for every 1 millisecond. In addition, the system acquires and records TOF mass spectrum of 60-microsecond length at sampling rate of 3 GS/s for every 1 millisecond without data processing. The system detects single ion signals from accumulated TOF mass spectrum of 10⁷ times and counts up to 10 ions accurately from a single event of TOF mass spectrum.     

Networking Mass Spectrometer Data Systems for Improved Productivity and Electronic Archiving of Data

Several Finngan-MAT mass spectrometer data systems were networked together to achieve the following two primary objectives: (1) to allow access to mass spectrometry data and data processing functions from remote locations without affecting simultaneous data acquisition at the instruments, and (2) to electronically archive mass spectrometry data at a central location on a high-capacity, fast-access device that allows rapid retrieval of archived data for all data processing operations at all locations. UNIX workstations, IBM PC/AT-compatible computers, and Data General Nova minicomputers were connected via Ethernet interfaces to allow rapid data transfer among all systems as well as X-Windows access to UNIX-based systems. Bridging techniques were used to isolate possible high-traffic areas of the network and to enable security measures for adequate protection of files. Additionally, serial connections were made through a Northern Telecom phone system to provide remote terminal access to the Data General Nova-based systems. Use of these connectivity techniques significantly improved productivity by allowing retrieval, processing, and printing of data from remote locations, such as office areas, without affecting data acquisition, processing, and printing performed simultaneously at the instruments. For archival purposes, data files are electronically stored on high-capacity magneto-optical disks for rapid retrieval. A highcapacity fixed disk is also available for centralized temporary data file storage. A Digital Equipment Corporation DECstation 2100 UNIX workstation was used as the file server for centralized data storage while being simultaneously utilized as the data system computer for one of the mass spectrometers. Utilization of this UNIX-based file server system in conjunction with Ethernet connectivity techniques provides a centralized, rapid-access, high-capacity, cost- and space-efficient method for electronic archival of mass spectrometry raw data recorded at all of the instruments.     

Simple,inexpensive mass spectrometric analyzer for thermogravimetry

A low‐cost mass spectrometer attachment for thermogravimetric analysis has been constructed from readily available commercial instruments and components. The benefits of this set‐up include excellent mass‐flow repeatability, simple design, and significantly lower adoption cost as opposed to ready‐built commercial solutions. The inclusion of an open source software package allows semi‐automated, highly simplified data analysis. The results from the instrument show excellent sensitivity for small volumes of evolved gas, as well as highly reproducible signal strengths. The GUI‐based software package provides data analysis in a way that is very intuitive and that can be easily modified to work with a broad range of TG instruments. Copyright © 2011 John Wiley & Sons, Ltd.     

A microcomputer-based system for the processing of spark-source mass spectrometry photoplates

A data acquisition system and processing software for spark-source mass spectrometry (s.s.m.s.) with photographic detection is described. The distinctive feature of this system is that data integrity is maintained during the acquisition and real-time reduction. A microprocessor is used to decide whether or not to save the incoming plate blackening data on a digital tape. This results in the selective recording of spectral lines while relatively long fields with only background are neglected. The magnetic tape is then processed on a general-purpose computer. As the complete profile of each peak is recorded, significant improvements can be made for the blackening linearization, the traceback of interferences and the mass calibration. The off-line software makes it possible not only to obtain the elemental sample composition but also to control the instrumental parameters and the photoplate characteristics. This renders the system suitable for research purposes as well as for routine analysis.     

An enhanced analytical strategy integrating offline two-dimensional liquid chromatography with high-resolution accurate mass spectrometry and molecular networking: Comprehensive characterization of HuangLian JieDu Decoction as a case study

Comprehensive ingredient research is of great significance for understanding the effective material basis of herbal medicines, but due to the diversity and complexity of their phytochemicals, such research is challenging. Here, a multifaceted strategy was proposed to analyze and identify the composition of HuangLian JieDu Decoction based on offline two-dimensional liquid chromatography combined with ultraviolet detection and high-resolution mass spectrometry. Multiple components were separated by two-dimensional liquid chromatography, which consisted of hydrophilic interaction chromatography and reversed-phase liquid chromatography, and then further characterized by high-resolution mass spectrometry with a full mass spectrometry/precursor ion list/data-dependent secondary scan data acquisition method. For data processing, database screening and molecular networking were used to identify the components in HuangLian JieDu Decoction. The offline two-dimensional liquid chromatography combined with ultraviolet detection and a high-resolution mass spectrometry system showed good orthogonality of 76.35% and a high peak capacity of 5175, effectively separating multiple components. Finally, 527 compounds, including 164 alkaloids, 133 terpenoids, 88 flavonoids, 60 phenylpropanoids, 38 organic acids, and 44 other compounds, were characterized. This integrated approach is suitable for the comprehensive characterization of herbal medicines and other complex chemical systems.     

High‐performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization,data management,and applications

The combination of high‐performance liquid chromatography and electrospray ionization ion mobility spectrometry facilitates the two‐dimensional separation of complex mixtures in the retention and drift time plane. The ion mobility spectrometer presented here was optimized for flow rates customarily used in high‐performance liquid chromatography between 100 and 1500 μL/min. The characterization of the system with respect to such parameters as the peak capacity of each time dimension and of the 2D spectrum was carried out based on a separation of a pesticide mixture containing 24 substances. While the total ion current chromatogram is coarsely resolved, exhibiting coelutions for a number of compounds, all substances can be separately detected in the 2D plane due to the orthogonality of the separations in retention and drift dimensions. Another major advantage of the ion mobility detector is the identification of substances based on their characteristic mobilities. Electrospray ionization allows the detection of substances lacking a chromophore. As an example, the separation of a mixture of 18 amino acids is presented. A software built upon the free mass spectrometry package OpenMS was developed for processing the extensive 2D data. The different processing steps are implemented as separate modules which can be arranged in a graphic workflow facilitating automated processing of data.     

An integrated method for metabolite detection and identification using a linear ion trap/Orbitrap mass spectrometer and multiple data processing techniques: application to indinavir metabolite detection

A new strategy using a hybrid linear ion trap/Orbitrap mass spectrometer and multiple post-acquisition data mining techniques was evaluated and applied to the detection and characterization of in vitro metabolites of indinavir. Accurate-mass, full-scan MS and MS/MS data sets were acquired with a generic data-dependent method and processed with extracted-ion chromatography (EIC), mass-defect filter (MDF), product-ion filter (PIF), and neutral-loss filter (NLF) techniques. The high-resolution EIC process was shown to be highly effective in the detection of common metabolites with predicted molecular weights. The MDF process, which searched for metabolites based on the similarity of mass defects of metabolites to those of indinavir and its core substructures, was able to find uncommon metabolites not detected by the EIC processing. The high-resolution PIF and NLF processes selectively detected metabolites that underwent fragmentation pathways similar to those of indinavir or its known metabolites. As a result, a total of 15 metabolites including two new indinavir metabolites were detected and characterized in a rat liver S9 incubation sample. Overall, these data mining techniques, which employed distinct metabolite search mechanisms, were complementary and effective in detecting both common and uncommon metabolites. In summary, the results demonstrated that this analytical strategy enables the high-throughput acquisition of accurate-mass LC/MS data sets, comprehensive search of a variety of metabolites through the post-acquisition processes, and effective structural characterization based on elemental compositions of metabolite molecules and their product ions.     

Real-life applications of the MULVADO software package for processing DOSY NMR data

MULVADO is a newly developed software package for DOSY NMR data processing, based on multivariate curve resolution (MCR), one of the principal multivariate methods for processing DOSY data. This paper will evaluate this software package by using real-life data of materials used in the printing industry: two data sets from the same ink sample but of different quality. Also a sample of an organic photoconductor and a toner sample are analysed. Compared with the routine DOSY output from monoexponential fitting, one of the single channel algorithms in the commercial Bruker software, MULVADO provides several advantages. The key advantage of MCR is that it overcomes the fluctuation problem (non-consistent diffusion coefficient of the same component). The combination of non-linear regression (NLR) and MCR can yield more accurate resolution of a complex mixture. In addition, the data pre-processing techniques in MULVADO minimise the negative effects of experimental artefacts on the results of the data. In this paper, the challenges for analysing polymer samples and other more complex samples will also be discussed.     

基于特征碎裂片段的葛根保健品中功效成分非定向筛查方法构建

通过超高效液相色谱-四极杆-静电场轨道阱高分辨质谱联用(UPLC-Q-Orbitrap HRMS),采用数据依赖采集模式对葛根保健品中15种功效成分的标准品进行分析,建立相应的标准谱库;对功效成分的断裂机理进行研究,得到其特征碎裂片段,并以数据非依赖型采集模式快速筛查葛根保健品中已知和未知的功效成分。15种功效成分在相应质量浓度范围内线性关系良好,相关系数(r~2)均大于0.99;不同加标水平下的回收率为83%～110%,相对标准偏差(RSD)为2.1%～8.6%。将该方法应用于实际样品分析,共筛查到16种功效成分,其中4种为所建标准谱库外的功效成分,表明所建方法可用于葛根保健品中功效成分的筛查。     

Package for on-line data acquisition and processing with microcomputers

Professor Ducauze and his co-workers from the Institut National Agronomique Paris-Grignon interfaced their CBM 8032 microcomputer with several chromatographs and developed a software package for the data acquisition and processing of the chromatograms. A specific option of the package is the correction of peak positions for long term drift by a comparison with reference chromatograms stored on disk.     

An Abel inversion method for radially resolved measurements in the axial injection torch

A method for the radial analysis of the plasma torch produced by the axial injection torch device at atmospheric pressure is proposed. The method uses a fast high-resolution acquisition set-up including an intensified charge coupled device and an image rotation system, as well as a new data processing procedure based on the Abel inversion technique that provides the radial profile of thin plasmas. Use of the Fernández-Palop smoothing technique significantly reduces distortion in the data profile. The accuracy of the proposed method was assessed by applying it to the estimation of the populations of HeI excited states.     

Enantioselective analysis of ketamine and its metabolites in equine plasma and urine by CE with multiple isomer sulfated beta-CD

CE with multiple isomer sulfated beta-CD as the chiral selector was assessed for the simultaneous analysis of the enantiomers of ketamine and metabolites in extracts of equine plasma and urine. Different lots of the commercial chiral selector provided significant changes in enantiomeric ketamine separability, a fact that can be related to the manufacturing variability. A mixture of two lots was found to provide high-resolution separations and interference-free detection of the enantiomers of ketamine, norketamine, dehydronorketamine, and an incompletely identified hydroxylated metabolite of norketamine in liquid/liquid extracts of the two body fluids. Ketamine, norketamine, and dehydronorketamine could be unambiguously identified via HPLC fractionation of urinary extracts and using LC-MS and LC-MS/MS with 1 mmu mass discrimination. The CE assay was used to characterize the stereoselectivity of the compounds' enantiomers in the samples of five ponies anesthetized with isoflurane in oxygen and treated with intravenous continuous infusion of racemic ketamine. The concentrations of the ketamine enantiomers in plasma are equal, whereas the urinary amount of R-ketamine is larger than that of S-ketamine. Plasma and urine contain higher S- than R-norketamine levels and the mean S-/R-enantiomer ratios of dehydronorketamine in plasma and urine are lower than unity and similar.     

Accurate mass measurement at enhanced mass-resolution on a triple quadrupole mass-spectrometer for the identification of a reaction impurity and collisionally-induced fragment ions of cabergoline

In this study, accurate mass measurements were made by electrospray ionization (ESI) on a triple quadrupole mass spectrometer operating in enhanced mass-resolution mode (peak width = 0.1 u FWMH), to give qualitative information relating to the pharmaceutical, cabergoline. Accurate mass determinations by ESI-MS were performed on a protonated impurity formed during cabergoline storage. The accurate mass measurement resulted in only one proposed elemental composition for the impurity, using reasonable elemental limits and mass tolerance for the calculation. This information was sufficient to propose a structure for the impurity where ESI-MS/MS proved consistent. The difference between the accurate mass measurement and the exact mass calculated for the proposed structure was 0.8 mmu, with a standard deviation of 0.7 mmu for replicate accurate mass determinations. Accurate mass determinations in ESI-MS/MS provided information on cabergoline fragment ions formed through collisionally-induced dissociation. Since the potential formation of isobaric ions exists for two major cabergoline fragment ions, accurate mass measurement allowed for the determination of the most probable fragment ion structures. The differences between the accurate mass measurements and exact masses calculated for the proposed fragment ions were 1.9 and 2.1 mmu, with standard deviations of 0.4 and 0.8 mmu, respectively, for replicate determinations.     

The rational use of a dynamic on-line data processing system for high and low resolution mass spectrometry

Some of the factors determining the configuration of a mass spectrometry data processing system are discussed. A rationalisation is given for a laboratory situation dealing with a variety of mass spectrometric problems. The effective use of a dynamic on-line system in such an environment is demonstrated. Conversational procedures are described for the acquisition, reduction and interpretation of mass spectral data, using a CRT visual display terminal as a fast man-computer interactive communication medium.