Retrieval of structure information from retention index

Integrative Profiling of Metabolites and Proteins

Methods such as mRNA expression profiling have provided a vast amount of genomic and transcriptomic information about plants and other organisms. However, there is explicit indication that considerable metabolic control is executed on the metabolite and on the protein level including protein modifications, thereby constituting the phenotypic plasticity. Consequently, the analysis of the molecular phenotype demands the step toward mass spectrometry (MS)-based postgenomic techniques such as metabolomics and proteomics. This chapter describes a straightforward protocol for simultaneously extracting metabolites and proteins from the same biological sample in preparation for MS analysis. Furthermore, protocols for profiling polar metabolites using gas chromatography time-of-flight MS and for shotgun proteomics using liquid chromatography-MS are discussed. A practical course is laid out that outlines all the basic steps, from harvesting to data analysis. These steps enable the correlative study of metabolite and protein dynamics with minimal technical variation. Biological variability of independent samples is exploited for variance analysis and pattern recognition.

Alkylphenol retention indices

A novel type of retention indices for alkylphenols and related compounds are proposed. The alkylphenol retention indices (APRI) use para-substituted n-alkylphenols as reference series. APRI for para-n-alkylphenols are per definition equal to the number of carbon atoms in the alkyl substituent; the value for phenol is zero. Application of the APRI system with different types of derivatisation of the phenolic hydroxy group showed that the derivatisation has limited influence on these indices. Especially para-substituted alkylphenols gave APRI values that could be transferred with high accuracy from one type of derivative to another. By comparing results obtained with different gradients in temperature-programmed GC, it was also shown that APRI is less affected by chromatographic conditions than retention indices based on n-alkanes.

Gas chromatographic retention indices for N-substituted amino s-triazines on capillary columns - Part IV: Influence of column polarity on retention index

The retention index increment for the addition of a methylene group to the alkyl group of an analyte molecule is shown to be lower than 100 i.u. for N-substituted amino s-triazines. In temperature programmed gas chromatography, a linearly interpolated retention index I, determined from the linear regression equation, I = AZ + (GRF)z, with the number of atoms (Z) in the molecule as variable, was used to describe the retention of 25 N-substituted amino s-triazines, on DB-1, DB-5 and DB-WAX capillary columns divided into five series according to the similarity of the alkyl groups in the particular series. In the above equation, A is the linear regression coefficient or the retention index increment per atom addition, Z the number of C,N and Cl atoms in the molecule, and (GRF)z the group retention factor or functionality constant for functional groups in the molecule, based on the number Z. It is possible to estimate the retention indices of an unknown member of the series from the Z, A and (GRF) values.

Improving the accuracy of Kováts' retention indices in isothermal gas chromatography

Isothermal Kováts' retention indices are currently reported as whole numbers, and are frequently deduced from a linear least mean squares fitting of the logarithms of adjusted retention times of a number of n-alkanes versus carbon number, following an iterative method that minimises errors. The currently accepted accuracy is about one retention index unit for apolar stationary phases, and lower for polar stationary phases. This paper presents results that show how the accuracy of the retention index may be safely reported to one-tenth of a retention index unit by the use of a non-linear equation, with present day gas chromatographs without electronic flow controllers. Results are presented that prove the correctness of the retention indices found for several substances on one particular capillary column. Hints on the minimum retention times needed to achieve the 0.1 retention index accuracy are mentioned, for retention times recorded in minutes and in seconds. According to results of this paper, two chromatograms, run under the appropriate conditions, are sufficient to obtain the desired accuracy. The method proposed in this paper does not require knowledge of the hold-up time of the chromatogram.

Quantitative structure-retention relationships for gas chromatographic retention indices of alkylbenzenes with molecular graph descriptors

Quantitative structure-retention relationships (QSRR) represent statistical models that quantify the connection between the molecular structure and the chromatographic retention indices of organic compounds, allowing the prediction of retention indices of novel, not yet synthesized compounds, solely from their structural descriptors. Using multiple linear regression, QSRR models for the gas chromatographic Kováts retention indices of 129 alkylbenzenes are generated using molecular graph descriptors. The correlational ability of structural descriptors computed from 10 molecular matrices is investigated, showing that the novel reciprocal matrices give numerical indices with improved correlational ability. A QSRR equation with 5 graph descriptors gives the best calibration and prediction results, demonstrating the usefulness of the molecular graph descriptors in modeling chromatographic retention parameters. The sequential orthogonalization of descriptors suggests simpler QSRR models by eliminating redundant structural information.

Prediction of retention indices. V. Influence of electronic effects and column polarity on retention index

The retention index increment for addition of a methylene group to an analyte molecule is shown for 1-halo-n-alkanes to be different from 100 i.u., a value that is customarily assigned according to the current convention in retention index prediction. In temperature-programmed gas chromatography using linearly interpolated retention index I, a linear regression equation, I=AZ+(GRF), with the number of atoms (Z) in the molecule as variable can describe the retention of 16 homologous series of organic compounds on non-polar and polar columns with characteristic A (linear regression coefficient) and (GRF) (group retention factor) values. A molecular model of retention on the basis of electron density and electron density distribution relative to that of n-alkane is proposed. This model brings out the inter- and intramolecular electronic effects in the analyte molecule and its dipole-dipole interaction with the stationary liquid phases, as variations in the A value. The (GRF) value varies with the connectivity ability of a functional group for extended conjugation, substitution, etc., but is most influenced by hydrogen bonding (H-bonding) with the stationary liquid phase. One can estimate the sequence of elution of a mixture of organic compounds from any two of the three parameters on the right-hand side of the above equation or retrieve the retention indexes of an entire homologous series from its A and (GRF) values. The fact that each analyte molecule has its own A value on different columns makes column difference (deltaI) compound-specific rather than column-specific, a departure from previous assumptions.