Method development databases

Zhang, S., Golbraikh, A., Oloff, S., Kohn, H., Tropsha, A. A novel automated lazy learning QSAR (ALL-QSAR) approach method development, applications, and virmal screening of chemical databases using validated ALL-QSAR models. 

Whereas the components of (known) test mixtures can be attributed on the basis of APCI+/, spectra, it is quite doubtful that this is equally feasible for unknown (real-life) extracts. Data acquisition conditions of LC-APCI-MS need to be optimised for existing universal LC separation protocols. User-specific databases of reference spectra need to be generated, and knowledge about the fragmentation rules of APCI-MS needs to be developed for the identification of unknown additives in polymers. Method development requires validation by comparison with established analytical tools. Extension to a quantitative method appears feasible. Despite the current wide spread of LC-API-MS equipment, relatively few industrial users, such as ICI, Sumitomo, Ford, GE, Solvay and DSM, appear to be somehow committed to this technique for (routine) polymer/additive analysis. 

It is generally difficult to identify developments with high potential where interferences do not preclude general application. To ensure the relevance of a method, its application to real sample analysis must be demonstrated. The accuracy of an analytical method should be confirmed by an independent method, or by the analysis of certified reference materials. Detailed comparative studies of the method developed with other well-established methods for polymer/additive analysis are not frequent in the analytical literature. Nevertheless, some examples may be found in Section 3.6. Improvements in analytical techniques are reasonably sought in sample preparation and in hyphenated chromatographic techniques. However, greatest efficiency is often gained from the use of databases rather than accelerated extraction or hyphenation. 

Compounds were optimized in positive ionization mode and in negative mode if necessary. Automaton can also perform automatic MS method development from solutions containing multiple compounds to increase throughput. When mixture solutions are used, Automaton injects a mixture once to determine all precursor ions and DP values and then injects once per compound to determine product ion and CE value. This approach allows automatic and unattended optimization of MS parameters for hundreds of compounds. The optimized parameters are stored in a compound database that permits fast and efficient retrieval of information about a specific compound and allows a compound to be used in multiple assays, eliminating the need to re-optimize the LC/MS/MS conditions. 

QuanOptimize from Micromass also allows automated method development for quantitative LC/MS/MS. It automatically identifies the best method for each compound, then runs batches of samples for quantitative analyses and report results in a QuanLynx browser. Thermo recently launched a similar product for automatic MS tuning. Known as QuickQuan, it generates data and stores it in a central Microsoft Access or Oracle database for future access. The infusion-based valve switching auto-tuning device allows individual compounds to be fully and automatically optimized in about 1 min. 

Many researchers have put a considerable amount of effort into studies of the chiral recognition mechanisms (using, e.g., NMR and molecular modeling), but yet the choice of chiral selector or chiral phase for a new compound is often based on trial and error. Different strategies for chiral method development have been presented by many of the retailers of chiral columns as a service for the customers. In addition to the information supplied by these retailers, another source of knowledge is Chirbase, a database that contains more than 50,000 HPLC separations of more than 15,000 different chiral substances [61], which also can provide guidance to the analytical chemist. 

As computers become more pervasive and increasingly powerful, specialized programs and databases are being developed to assist in a wide variety of research efforts. This is true in the search for solvent alternatives, and in this section we review the application of computers to solvent substitution studies and cover computer-aided molecular design of new solvents, methods developed for the prediction of physical properties, methods for predicting less precise chemical characteristics such as toxicity and carcinogenicity, and computer-aided design of alternative synthetic pathways. 

The advantage of generic LC/MS run conditions is that it allows the preparation of an LC/MS separation database that can be referenced for compound mixtures from anywhere in the development and manufacturing process cycle. It trades off resolution for consistency, speed, and a decrease in methods development times. It permits creation of a computer-searchable database of information for all of the compounds being investigated in the company. The mass spectrometer provides sensitivity and resolution gain as well as information on retention times and molecular weights. 

Standard methods Template structure identification Databases Method development (molecular structure) Qualitative and quantitative analysis... 

FJ clusters (in FJ units, or as a model for specified rare-gas atom clusters) continue to be used as a benchmark system for verification and tuning in method development. With the work of Romero et al. [52], there are now proposed global minimum structures and energies available on the internet [53], up to n=309. This considerably extends the Cambridge cluster database [54], but the main body of data comes from EA work that used the known FJ lattices (icosahedral, decahedral, and face-centered cubic) as the input. This is obviously dangerous,... 

Application databases have been particularly popular in the world of chiral method development (Figure 10-5). While it has been observed that small changes in compounds can result in loss of effectiveness (separation selectivity) for a given method, the results of searches can be used to create targeted method screens that can reduce the time and expense of development [36]. 

The TAE/RECON method, developed by Breneman and co-workers based on Bader s quantum theory of Atoms In Molecules (AIM). The TAB method of molecular electron density reconstruction utilizes a library of integrated atomic basins , as defined by the AIM theory, to rapidly reconstruct representations of molecular electron density distributions and van der Waals electronic surface properties. RECON is capable of rapidly generating 6-31-I-G level electron densities and electronic properties of large molecules, proteins or molecular databases, using TAB reconstruction. A library of atomic charge density fragments has been assembled in a form that allows for the rapid retrieval of the fragments, followed by rapid molecular assembly. Additional details of the method are described elsewhere. ... 

All the methods developed so far try to extract information, directly or indirectly (Lim, 1974), from the ever growing databases of X-ray crystallography resolved protein structures. Unfortunately, the rate at which new structures are added to the structure databases is far from optimal. Chothia (1992) estimated that all proteins, when their structures are known, would fall into about one thousand folding classes, more than half of them yet to be discovered. If so, this means that a great deal of information in the forthcoming structures is not available for the current methods, and therefore we still must rely on the future to see a coherent and realistic increase in the accuracy of secondary structure prediction methods. 

Trace analysis and the move to the use of smaller sample sizes represent particular challenges in that the ratio of surface area exposure to sample volume, or quantity of analyte, is increased, multiplying the possible effect and level of contamination. While mass spectral identification of contaminants will aid in identifying their source (see the literature-derived Excel database of contaminant mass spectra in the supplementary data of Keller et al 12), this is not essential. The key tool to their elimination is the appropriate use of sample blanks at each step of the analytical protocol during method development and validation. 

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