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Background In proteomics studies, liquid chromatography coupled to mass spectrometry (LC-MS) has proven to be a powerful technology to investigate differential expression of proteins/peptides that are characterized by their peak intensities, mass-to-charge ratio (m/z), and retention time (RT). The variable complexity of peptide mixtures and occasional drifts lead to substantial variations in m/z and RT dimensions. Thus, label-free differential protein expression studies by LC-MS technology require alignment with respect to both RT and m/z to ensure that same proteins/peptides are compared from multiple runs. Methods In this study, we propose a new strategy to align LC-MALDI-TOF data by combining quality threshold cluster analysis and support vector regression. Our method performs alignment on the basis of measurements in three dimensions (RT, m/z, intensity). Results and conclusions We demonstrate the suitability of our proposed method for alignment of LC-MALDI-TOF data through a previously published spike-in dataset and a new in-house generated spike-in dataset. A comparison of our method with other methods that utilize only RT and m/z dimensions reveals that the use of intensity measurements enhances alignment performance.

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In continuum mechanics, the most commonly used measure of stress is the Cauchy stress tensor, often called simply the stress tensor or "true stress". However, several alternative measures of stress can be defined:[1][2][3]

Analysis of exhaled breath samples reveals the presence of many volatile organic compounds (VOCs). The VOC composition of the breath, the so-called breath profile, contains a variety of information including the health status and condition of the organism that...

ABSTRACT Bifidobacteria are a major microbial component of infant gut microbiota, which is believed to promote health benefits for the host and stimulate maturation of the immune system. Despite their perceived importance, very little is known about the ...

Abstract. Summary: Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such

Two different algorithms for time‐alignment as a preprocessing step in linear factor models are studied. Correlation optimized warping and dynamic time warping are both presented in the literature as methods that can eliminate shift‐related artifacts from measurements by correcting a sample vector towards a reference. In this study both the theoretical properties and the practical implications of using signal warping as preprocessing for chromatographic data are investigated. The connection between the two algorithms is also discussed. The findings are illustrated by means of a case study of principal component analysis on a real data set, including manifest retention time artifacts, of extracts from coffee samples stored under different packaging conditions for varying storage times. We concluded that for the data presented here dynamic time warping with rigid slope constraints and correlation optimized warping are superior to unconstrained dynamic time warping; both considerably simplify interpretation of the factor model results. Unconstrained dynamic time warping was found to be too flexible for this chromatographic data set, resulting in an overcompensation of the observed shifts and suggesting the unsuitability of this preprocessing method for this type of signals. Copyright © 2004 John Wiley & Sons, Ltd.

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Correlation optimized warping has been the most used technique to correct the drifts in peak positions. COW aligns the unaligned chromatogram to the reference chromatogram provided slack (t) and segment lengths (m) are optimized. However, several combinations of m and t need to be tested before finding the o

The Visual Computer - Retrieval and comparative editing/modeling of motion data require temporal alignment. In other words, for such processes to perform accurately, critical features of motion...

Prediction of Total Phenolic Content in Extracts of Prunella Species from HPLC Profiles by Multivariate Calibration

The U.S. Department of Energy's Office of Scientific and Technical Information

Purpose: In computed tomographic colonography (CTC), a patient will be scanned twice—Once supine and once prone—to improve the sensitivity for polyp detection. To assist radiologists in CTC reading, in this paper we propose an automated ...

Introduction to RGCxGC package

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