iMatch: A retention index tool for analysis of gas chromatography–mass spectrometry data

Abstract

A method was developed to employ National Institute of Standards and Technology (NIST) 2008 retention index database information for molecular retention matching via constructing a set of empirical distribution functions (DFs) of the absolute retention index deviation to its mean value. The effects of different experimental parameters on the molecules’ retention indices were first assessed. The results show that the column class, the column type, and the data type have significant effects on the retention index values acquired on capillary columns. However, the normal alkane retention index (Inorm) with the ramp condition is similar to the linear retention index (IT), while the Inorm with the isothermal condition is similar to the Kováts retention index (I). As for the Inorm with the complex condition, these data should be treated as an additional group, because the mean Inorm value of the polar column is significantly different from the IT. Based on this analysis, nine DFs were generated from the grouped retention index data. The DF information was further implemented into a software program called iMatch. The performance of iMatch was evaluated using experimental data of a mixture of standards and metabolite extract of rat plasma with spiked-in standards. About 19% of the molecules identified by ChromaTOF were filtered out by iMatch from the identification list of electron ionization (EI) mass spectral matching, while all of the spiked-in standards were preserved. The analysis results demonstrate that using the retention index values, via constructing a set of DFs, can improve the spectral matching-based identifications by reducing a significant portion of false-positives.

Olanzapine Activates Hepatic Mammalian Target of Rapamycin: New Mechanistic Insight into Metabolic Dysregulation with Atypical Antipsychotic Drugs

“…For metabolite identification using ChromaTOF, each chromatographic peak was tentatively assigned to a metabolite if its experimental mass spectrum and a database spectrum have a spectral similarity score no less than 600. The retention index matching in MetPP was performed using the iMatch method with the P value threshold set as P # 0.001 (Zhang et al, 2011). The pairwise two-tail t test was used to determine whether a metabolite had a statistically significant abundance difference between sample groups by setting the threshold of false discovery rate q # 0.3.…”

Chromatographic retention indices in identification of chemical compounds

“…Procedures for determination of RI search windows (RI thresholds) were considered in several articles [43][44][45][46]. Barnes et al [47] suggested a methodology called "retention projection", which can overcome the limitations of shared chromatographic databases, such as a relatively large spread of retention data in different databases.…”

MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics

“…Currently, MetPP can perform retention index matching only for the first dimensional GC. We improved the algorithms of iMatch approach (Zhang et al, 2011) by enabling retention index matching of multiple top-ranked identification results, to ensure that the true metabolite can still be preserved even though it may not have the best score for mass spectral matching (Koo et al, 2011). We further updated the retention index database used in iMatch to NIST11 retention index database and calculated all retention index distributions.…”