As FIA-MS and liquid chromatography mass spectrometry (LC-MS) become more pervasive in the analysis of compound libraries, open-access instrumentation is increasingly used in HTOS laboratories as well as in support of general medicinal chemistry. These open-access systems are most often used for reaction monitoring and optimization, and in some cases, for library quality control and synthesis product purification.
The first open-access systems were described by Pullen et al.  and Taylor et al. . These systems were based on FIA-MS or generic LC-MS analysis with single quadrupole mass spectrometers to ensure the ease of use and ruggedness of the system. Spreen et al.  also described an open-access facility. The use of the open-access facility has increased sample throughput by 60% and has allowed the mass spectrometrists to spend more time on nonroutine problems. Mallis et al.  described an open-access facility in a drug-discovery environment that was comprised of FIA-MS and LC-MS units to monitor synthetic chemistry reactions as well as the integrity and purity of new chemical entities. Greaves  described an open-access mass spectrometry in an academic environment, primarily in support of organic synthesis but also for the use of biological scientists. The open-access methods featured FIA-MS, gas chromatography mass spectography (GC-MS), and MALDI-TOF-MS systems, as well as autosamplers with plate-handling interfaces. This level of automation allows access to the instruments by a user community of more than 100 users, day or night.
Automation of data acquisition, processing, interpretation, and reporting is another trend in the effort to improve the throughput of compound library analysis. Daley et al.  reported automated high throughput LC-MS methods for verification of library compound structure from 96 wells. Greig  reported an automated procedure for the calculation and storage of sample purity information based on the LC-MS results. The combination of a fast LC-MS method and automated data-processing techniques enabled high throughput analysis of combinatorial library samples at the rate of up to 2300 per week per instrument. Tong et al.  developed hardware components and software modules to enhance the automation, efficiency, and reliability of a commercial open-access FIA-MS system. The software modules include utilities for data manipulation/reduction, data interpretation, data transmission, and reporting to the desktop computer of the submitter. Choi et al. [38,39] reported an approach to apply intelligent automation for high throughput LC-MS analysis of compound libraries with Microsoft Visual Basic software. Compounds were analyzed by a generic primary HPLC method. Those that failed, in the initial analysis, were reanalyzed automatically with secondary analytical methods based on the information derived from the target analyte structure. Examples were described where a secondary method with a longer column and slower gradient was selected for target compounds that failed in primary analysis with ClogP values less than one. Williams et al.  reported an automated molecular-weight assignment method for positive-ion ESI-MS spectra. The software application (MassAssign) differentiates [M + H]+ ions from other signals in a complex mass spectrum and reports assignments in the form of either a single component that has the displayed molecular weight, multiple components, or an undetermined molecular weight. Initial tests with the program yielded a 90% success rate compared with manual interpretation for 55 samples . Yates et al.  reported a method of rapid characterization of multi- or single-component libraries. The methodology compares LC-MS analysis results with predicted ESI mass spectra to confirm library products, identify chemical-synthesis errors, and assess overall library integrity. In general, equal signal intensities were observed for most combinatorial mixture components, and indicated that differences in ESI efficiency was not a major limitation to this approach. High throughput data-processing programs and informatics tools were used to speed data analysis and simplify the presentation of the library characterization results. Potential limitations of the method include unequal sensitivity of library members and multiply charged-ion formation for large compounds. Klagkou et al. reported an initial study on the determination of the fragmentation rules for some classes of compounds in ESI tandem mass spectrometry (MS/MS). Based on studies carried out on several combinatorial libraries, it was established that different classes of drug molecules follow unique fragmentation pathways. The results were incorporated into an artificial intelligence (AI) software package with the goal of addressing the issue of high throughput, automated MS/MS data interpretation .
Automated data processing, data reduction, spectral interpretation, and reporting are also integral parts of open-access sample analysis. Mallis et al.  described the use of an open-access system with e-mail capabilities to distribute processed data reports to the chemist. Several methods have been developed, including structure elucidation with in-source collision-induced dissociation (CID).
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