Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires new data preprocessing approaches to correlate specific metabolites to their biological origin. Here we introduce an LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching. Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a nonlinear retention time correction profile for each sample. Following retention time correction, the relative metabolite ion intensities are directly compared to identify changes in specific endogenous metabolites, such as potential biomarkers. The software is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples. XCMS is freely available under an open-source license at http://metlin...

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.

The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to the classical methods of differential protein gel or blot staining by dyes and fluorophores, mass-spectrometry-based quantification methods have gained increasing popularity over the past five years. Most of these methods employ differential stable isotope labeling to create a specific mass tag that can be recognized by a mass spectrometer and at the same time provide the basis for quantification. These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic peptide standards. In contrast, label-free quantification approaches aim to correlate the mass spectrometric signal of intact proteolytic peptides or the number of peptide sequencing events with the relative or absolute protein quantity directly. In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data.

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Quantitative mass spectrometry in proteomics: a critical review

Dynamic Time Warping (DTW) has a quadratic time and space complexity that limits its use to small time series. In this paper we introduce FastDTW, an approximation of DTW that has a linear time and space complexity. FastDTW uses a multilevel approach that recursively projects a solution from a coarser resolution and refines the projected solution. We prove the linear time and space complexity of FastDTW both theoretically and empirically. We also analyze the accuracy of FastDTW by comparing it to two other types of existing approximate DTW algorithms: constraints (such as Sakoe-Chiba Bands) and abstraction. Our results show a large improvement in accuracy over existing methods.

/pdf/toward-accurate-dynamic-time-warping-in-linear-time-and-3p0rzztewt.pdf

Toward accurate dynamic time warping in linear time and space

Quality control of herbal medicines

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography - mass spectrometry data

Gunnar Malmquist

Papers

Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography - mass spectrometry data

Analysis of complex protein elution behavior in preparative ion exchange processes using a colloidal particle adsorption model