Hierarchically structured computer systems for analytical chemistry

For the Max-Planck-Institutes in Mülheim (Germany) a new centralized computer system has been designed and brought into operation in 1981. The system is built from two VAX 11/780 computers sharing peripheral resources. Experimental data from remote analytical instruments are gathered in real-time via satellite processors connected with coaxial cables and DMA-interfaces to the central computers. Several other small computer systems are transferring completed data files via asynchroneous serial lines.This centralized system is used for all kind of computer applications of the two institutes: for quantum chemical calculations, X-ray structure determinations, spectrometry and chromatography as well as for chemical literature search, text processing, administrative tasks, etc. The essential criteria for designing and using this or similar structured systems are discussed.

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Hierarchisch aufgebaute Rechnersysteme für die Analytik

     

Practical approach to archival and retrieval of analytical data in the laboratory

Today's analytical laboratory uses a large number of different instruments that are connected in networks. Together with increasing automation, data are produced at a rate that can easily reach gigabytes per month, which generates the problem of systematic archival. In addition, working under Good Laboratory Practice requires that archival of raw data be performed in such a way that they can be readily retrieved upon request, even years later. While systematic archival of data is already performed in most laboratories, it is the retrieval of saved information that is often far from straightforward. This paper describes a simple but systematic approach for both archival and retrieval of data files and related electronic documents. It consists of an unambiguous scheme for the naming of electronic files, an efficient backup strategy, a simple database holding information about any data acquired, and a convenient interface to this database that can be accessed from any workplace while assuring restricted access. The system is capable of handling several databases concurrently and is used in our facility to archive data from several workgroups. The use of freely available software such as the Linux operating system made it possible to implement a fast and stable solution at exceptionally low cost.     

Non-electrophoretic differential detergent fractionation proteomics using frozen whole organs

Non-electrophoretic methods based on two-dimensional liquid chromatography followed directly by tandem mass spectrometry (2D-LC/MS(2)) have become the preferred method for high-throughput expression proteomics and are widely applied to fresh tissues. Pre-fractionation techniques are also used in combination with 2D-LC/MS(2) to both increase the proteome size and to assign cellular locations. Data from such experiments have become central to systems biology analyses. Here we apply a differential detergent (pre)fractionation (DDF) followed by 2D-LC/MS(2) to frozen archival tissues. Our results show that by using frozen archival tissues, we do not lose proteome coverage or the ability to assign proteins to cellular compartments. In addition, we were able to assign 'biological process' Gene Ontology (GO) annotations, which will facilitate systems biological modeling of our proteomics data.     

Operation of an academic open access mass spectrometry facility with particular reference to the analysis of synthetic compounds

Open access mass spectrometry now provides the opportunity to move this spectroscopic method to the beginning of the analytical chain, a place formerly the exclusive province of NMR and TLC. To date this transition has been occurring in industrial settings but there has been less change in the academic environment. This paper provides one blueprint for setting up such a facility, primarily in support of organic synthesis but also for the use of biological scientists. The open access format used at UCI utilizes four instruments: an ESI-TOFMS system used in the flow injection mode, two GC/MS systems (one in EI and one in CI) and a MALDI-TOFMS system. The first three instruments have autosamplers and open access software whereas the MALDI system has a fully automated plate handling interface. This level of automation allows access to the instruments by a user community of more than 100 users, day or night. The decisions made in setting up these instruments were based on a 'keep it simple' philosophy, given the fact that the primary type of data of interest is the molecular mass of the analyte and that data are required for a very wide range of structures.     

An efficient data format for mass spectrometry-based proteomics

The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems.     

Three-dimensional concentration mapping of gases using a portable mass spectrometer system

The visualization of hazardous gaseous emissions at volcanoes using in-situ mass spectrometry (MS) is a key step towards a better comprehension of the geophysical phenomena surrounding eruptive activity. In-situ data consisting of helium, carbon dioxide, sulfur dioxide, and other gas species, were acquired with a quadrupole based MS system. Global position systems (GPS) and MS data were plotted on ground imagery, topography, and remote sensing data collected by a host of instruments during the second Costa Rica Airborne Research and Technology Applications (CARTA) mission. This combination of gas and imaging data allowed three-dimensional (3D) visualization of the volcanic plume and the mapping of gas concentration at several volcanic structures and urban areas. This combined set of data has demonstrated a better tool to assess hazardous conditions by visualizing and modeling of possible scenarios of volcanic activity. The MS system is used for in-situ measurement of 3D gas concentrations at different volcanic locations with three different transportation platforms: aircraft, auto, and hand-carried. The demonstration for urban contamination mapping is also presented as another possible use for the MS system.     

Complex mixture analysis based on gas chromatography-mass spectrometry with time array detection using a beam deflection time-of-flight mass spectrometer

A beam deflection time-of-flight mass spectrometer was developed in conjunction with an integrating transient recorder to provide time array detection, permitting high mass spectral scan file acquisition rates for complex mixture analysis by capillary gas chromatography-mass spectrometry (GC-MS). Results are presented for the analysis of a urinary organic acid mixture by GC-MS at a scan file acquisition rate of 10 scan files per second (sf/s), showing the advantages of such data collection in the deconvolution of partially resolved components. The reconstructed total ion current (RTIC) chromatogram available from data acquired at this scan file generation rate is shown to be comparable to the profile obtained from a flame ionization detector in representing the chromatography performed under identical experimental parameters. The RTIC chromatogram available from the database obtained at 10 sf/s is compared with that available from a database obtained at 1 sf/s, the latter representing that scan rate typically used with most GC-MS instruments. The advantages of the higher scan file acquisition rate in representing the chromatographic profile and in allowing mass spectral data to be obtained for components in the complex mixture that are unresolved chromatographically are discussed.     

Mass spectrometry in the U.S. space program: Past, present, and future

Recent years have witnessed significant progress on the miniaturization of mass spectrometers for a variety of field applications. This article describes the development and application of mass spectrometry (MS) instrumentation to support of goals of the U.S. space program. Its main focus is on the two most common space-related applications of MS: studying the composition of planetary atmospheres and monitoring air quality on manned space missions. Both sets of applications present special requirements in terms of analytical performance (sensitivity, selectivity, speed, etc.), logistical considerations (space, weight, and power requirements), and deployment in perhaps the harshest of all possible environments (space). The MS instruments deployed on the Pioneer Venus and Mars Viking Lander missions are reviewed for the purposes of illustrating the unique features of the sample introduction systems, mass analyzers, and vacuum systems, and for presenting their specifications which are impressive even by today's standards. The various approaches for monitoring volatile organic compounds (VOCs) in cabin atmospheres are also reviewed. In the past, ground-based GC/MS instruments have been used to identify and quantify VOCs in archival samples collected during the Mercury, Apollo, Skylab, Space Shuttle, and Mir missions. Some of the data from the more recent missions are provided to illustrate the composition data obtained and to underscore the need for instrumentation to perform such monitoring in situ. Lastly, the development of two emerging technologies, Direct Sampling Ion Trap Mass Spectrometry (DSITMS) and GC/Ion Mobility Spectrometry (GC/IMS), will be discussed to illustrate their potential utility for future missions.     

Calculation of the information content of retrieval procedures applied to mass spectral data bases

A procedure has been developed for estimating the information content of retrieval systems with binary-coded mass spectra, as well as mass spectra coded by other methods, from the statistical properties of a reference file. For a reference file, binary-coded with a threshold of 1% of the intensity of the base peak, this results typically in an estimated information content of about 50 bits for 200 selected $\text{m}\text{z}$ values. It is shown that, because of errors occurring in the binary-coded spectra, the actual information content is only about 12 bits. This explains the poor performance observed for retrieval systems with binary-coded mass spectra.     

Distributed data processing in NMR spectroscopy

The development and use of a communication system for the chemical laboratory is described. It provides local access to instruments, computers and personal work stations (PC) as well as connection to wide area networks via the X.25 standard protocol and respective gateways on the basis of the DFN services (Deutsches Forschungsnetz) dialog, remote job entry, file transfer and message handling (EAN X.400). The standardization of digital spectra is considered.     

Examples of Fourier transform ion cyclotron resonance mass spectrometry developments: from ion physics to remote access biochemical mass spectrometry

The application of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) for high resolution biomolecular analysis has increased greatly after 30 years of innovation since its conception in 1974. FT- ICR-MS can now routinely be used for the analysis of complex organic mixtures such as biological or petrochemical samples. Many of these new possibilities have been the results of many different instrumental developments. This paper provides a mini review of selected instrumental developments that now allow these measurements. The development of soft ionization techniques such as electrospray ionization and matrix assisted laser desorption and ionisation was crucial for the analysis of biological macromolecules. Improved ion transport optics led to an increase in sensitivity. New ICR cell designs complement the capabilities of FT-ICR-MS by allowing a more thorough study of the mechanism and kinetics of ion reactions in the gas-phase. A selected example of electron capture dissociation (ECD) employs these developments to investigate the role of peptide conformation in ECD. Improved electronics and software allow faster and more flexible experiments. All these improvements led to an increase in speed and sensitivity that are necessary to couple FT-MS to fast separation techniques such as nano-high performance liquid chromatography. The modern FT-ICR-MS instruments can be incorporated in virtual organizations allowing remote access to unique infrastructure. This concept of remote experimentation opens new possibilities for scientific collaborations between expert scientists at different locations and allows the efficient use of this expensive instrumentation.     

Search strategy and data compression for a retrieval system with binary-coded mass spectra

A retrieval system for binary-coded mass spectra is described. The data base used contains 9628 low-resolution mass spectra from the Aldermaston Mass Spectra Data Collection. These spectra are reduced to 106 preselected binary-coded m/z values each. Storage of the compound names and formulae is minimized by using a special set of characters and file organization. The search strategy permits fast generation of the N- nearest neighbours. Depending on the number of best matches generated, an average search requires access to only 24—33% of the spectra contained in the data base. Because of its limited storage requirements, this search system can be used even on microcomputers.l]     

Automated mass correction and data interpretation for protein open-access liquid chromatography-mass spectrometry

Characterization of recombinant protein purification fractions and final products by liquid chromatography-mass spectrometry (LC/MS) are requested more frequently each year. A protein open-access (OA) LC/MS system was developed in our laboratory to meet this demand. This paper compares the system that we originally implemented in our facilities in 2003 to the one now in use, and discusses, in more detail, recent enhancements that have improved its robustness, reliability, and data reporting capabilities. The system utilizes instruments equipped with reversed-phase chromatography and an orthogonal accelerated time-of-flight mass spectrometer fitted with an electrospray source. Sample analysis requests are accomplished using a simple form on a web-enabled laboratory information management system (LIMS). This distributed form is accessible from any intranet-connected company desktop computer. Automated data acquisition and processing are performed using a combination of in-house (OA-Self Service, OA-Monitor, and OA-Analysis Engine) and vendor-supplied programs (AutoLynx, and OpenLynx) located on acquisition computers and off-line processing workstations. Analysis results are then reported via the same web-based LIMS. Also presented are solutions to problems not addressed on commercially available, small-molecule OA-LC/MS systems. These include automated transforming of mass-to-charge (m/z) spectra to mass spectra and automated data interpretation that considers minor variants to the protein sequence-such as common post-translational modifications (PTMs). Currently, our protein OA-LC/MS platform runs on five LC/MS instruments located in three separate GlaxoSmithKline R&D sites in the US and UK. To date, more than 8000 protein OA-LC/MS samples have been analyzed. With these user friendly and highly automated OA systems in place, mass spectrometry plays a key role in assessing the quality of recombinant proteins, either produced at our facilities or bought from external sources, without dedicating extensive amounts of analyst resource.     

Data Processing for 3D Mass Spectrometry Imaging

Data processing for three dimensional mass spectrometry (3D-MS) imaging was investigated, starting with a consideration of the challenges in its practical implementation using a series of sections of a tissue volume. The technical issues related to data reduction, 2D imaging data alignment, 3D visualization, and statistical data analysis were identified. Software solutions for these tasks were developed using functions in MATLAB. Peak detection and peak alignment were applied to reduce the data size, while retaining the mass accuracy. The main morphologic features of tissue sections were extracted using a classification method for data alignment. Data insertion was performed to construct a 3D data set with spectral information that can be used for generating 3D views and for data analysis. The imaging data previously obtained for a mouse brain using desorption electrospray ionization mass spectrometry (DESI-MS) imaging have been used to test and demonstrate the new methodology.     

OmniSpect: An Open MATLAB-Based Tool for Visualization and Analysis of Matrix-Assisted Laser Desorption/Ionization and Desorption Electrospray Ionization Mass Spectrometry Images

We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.      

基于化学计量学的通用化学数据采集处理系统

研制开发基于化学计量学的通用化学数据采集处理系统，该系统硬件采集部分，可与模拟信号输出的分析仪器或有RS－232接口的分析仪器联接进行数据采集，软件部分的数据处理基于化学计量学理论知识，相应数据处理方法，可从采集到数据中获取大量的信息。软件部分的信息管理包含了大量实验要素的归整、查询和统计等。     

NMF-Based Approach for Missing Values Imputation of Mass Spectrometry Metabolomics Data

In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data. The proposed method was compared with three commonly used methods: k-nearest neighbors (kNN), random forest (RF), and outlier-robust (ORI) missing values imputation. These methods were evaluated from the perspectives of accuracy of imputation, retrieval of data structures, and rank of imputation superiority. The experimental results showed that the NMF-based method is well-adapted to various cases of data missingness and the presence of outliers in MS-based metabolic profiles. It outperformed kNN and ORI and showed results comparable with the RF method. Furthermore, the NMF method is more robust and less susceptible to outliers as compared with the RF method. The proposed NMF-based scheme may serve as an alternative NA imputation method which may facilitate biological interpretations of metabolomics data.     

Fabrication of polymer microsphere particle standards containing trace explosives using an oil/water emulsion solvent extraction piezoelectric printing process

We present a methodology for fabricating polymer microspheres using inkjet printing of a biodegradable polymer containing either high explosives or high explosive simulant. Poly(dl-lactide/glycolide) 85:15 (PLGA) microsphere production is based on an oil/water emulsion solvent extraction process. The inkjet printing process allows for precise control of the microsphere diameter and the chemical composition. The microspheres can be used as calibrants or verification standards for explosives trace detection instruments. Gas chromatography/mass spectrometry analysis demonstrated that the composition of the microspheres was consistent with predicted concentrations based on the amount of analyte incorporated into the polymer solution and the inkjet operating parameters. We have demonstrated that the microspheres can be fabricated with a mass fraction of 70% of an analyte compound.     

MS-IAS:集成的质谱代谢组学数据分析系统

针对代谢组学研究中的数据处理问题,本研究建立了基于质谱的数据分析系统MS-IAS(Mass spectrometry based integrated analysis system).此系统集成了特征选择、聚类、分类等多种方法,用以处理质谱数据,具有多种统计分析方法能对所选的特征变量进行比较,以发现与所研究问题相关的潜在生物标志物.MS-IAS支持数据与多种算法结果可图形化显示,有助于对数据的解释与分析.以肝病患者的质谱代谢组数据为例,展示MS-IAS的功能,两种特征选择算法从数据集中筛选出了40个对肝病具有区分能力的特征变量,展示了MS-IAS成为代谢组学研究中的通用质谱数据分析系统的潜力.     

The development of fieldable laser-induced breakdown spectrometer: No limits on the horizon

In this review, new trends in the development of fieldable instrumentation based on laser-induced breakdown spectroscopy (LIBS) and its recent applications is presented. Depending on the LIBS configuration we will distinguish between portable, remote and stand-off instruments. Moreover, the development of portable systems gives greater flexibility and also increases the range of LIBS applications. In general, portable instruments are employed in close-contact applications like immovable artworks, contaminated soils and environmental diagnostic, while remote and stand-off instruments are normally used in analytical applications at distances where access to the sample is difficult or hazardous. Although remote and stand-off instruments are both used for chemical analysis at distances, the instrumental configurations are completely different. In remote analysis, an optical fiber is employed to deliver the laser energy a certain distance. This approach has been usually restricted to industrial applications, bulk analysis in water, geological measurements and chemical analysis on nuclear stations. In the case of stand-off applications, the laser beam and the returning plasma light are transmitted in an open-path configuration. In this article we also discuss the instrumental requirements in the design of remote and stand-off instruments.