MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts.

Variable reference alignment: an improved peak alignment protocol for NMR spectral data with large intersample variation.

In an effort to address the variable correspondence problem across large sample cohorts common in metabolomic/metabonomic studies, we have developed a prealignment protocol that aims to generate spectral segments sharing a common target spectrum. Under the assumption that a single reference spectrum will not correctly represent all spectra of a data set, the goal of this approach is to perform local alignment corrections on spectral regions which share a common "most similar" spectrum. A natural beneficial outcome of this procedure is the automatic definition of spectral segments, a feature that is not common to all alignment methods. This protocol is shown to specifically improve the quality of alignment in (1)H NMR data sets exhibiting large intersample compositional variation (e.g., pH, ionic strength). As a proof-of-principle demonstration, we have utilized two recently developed alignment algorithms specific to NMR data, recursive segment-wise peak alignment and interval correlated shifting, and applied them to two data sets composed of 15 aqueous cell line extract and 20 human urine (1)H NMR profiles. Application of this protocol represents a fundamental shift from current alignment methodologies that seek to correct misalignments utilizing a single representative spectrum, with the added benefit that it can be appended to any alignment algorithm.

Antioxidant and immunobiological activity of water-soluble polysaccharide fractions purified from Acanthopanax senticosu.

A water-soluble polysaccharide obtained from Acanthopanax senticosus leaves (ASL), was fractionated by DEAE-Sepharose fast-flow column chromatography, and purified by Sephadex G-75 gel-permeation column chromatography. The characteristics of ASP-2-1 were determined by chemical analysis, high-performance capillary electrophoresis (HPCE), high-performance gel-permeation chromatography (HPGPC). The results show that ASP-2-1 contained 89.47% carbohydrate, 7.45% uronic acid, 2.16% protein and seven kinds of monosaccharides including rhamnose, xylose, glucose, mannose, arabinose, galactose and glucuronic acid in a molar ratio of 7.45:18.63:25.15:0.93:8.35:2.79:5.69, with an average molecular weight of about 14,573Da. Furthermore, the immunobiological and antioxidant activities, in vitro, of ASP-2-1 were evaluated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay and ferric-reducing antioxidant power assay (FRAP), 2,2-diphenyl-1-picrylhydrazyl (DPPH()), superoxide radical (()O(2)(-)) and hydroxyl radical (()OH) free radical-scavenging assay, respectively. The results showed that ASP-2-1 exhibited significantly higher immunomodulatory activities against the lymphocyte proliferation in vitro, pronounced reductive power (FRAP value: 785.1µM at 0.2mg/ml), strong hydroxyl radical (89.56% at 1mg/ml) scavenging activity, moderate superoxide radicals (65.32% at 1mg/ml) and DPPH radicals (68.9% at 1mg/ml) scavenging activities. ASP-2-1 should be explored as a novel and potential natural antioxidant and immunostimulating agent for use in functional foods or medicine.