Coherent point drift peak alignment algorithms using distance and similarity measures for two‐dimensional gas chromatography mass spectrometry data

Li, Zeyu; Kim, Seongho; Zhong, Sikai; Zhong, Zichun; Kato, Ikuko; Zhang, Xiang

doi:10.1002/cem.3236

Cited by 7 publications

(4 citation statements)

References 24 publications

(46 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to mitigate peak shift problems, several methods have been reported to be useful. Automatic time shift alignment (ATSA) [21], coherent point drift peak alignment [22], Global peak alignment with point matching algorithm [23], and PARAFAC Applied to Shift Invariant Amplitude Spectra (PARASIAS) [24] are among the techniques that have demonstrated effectiveness in aligning peaks accurately despite shifts or distortions. Derivative calculation of spectral data is a promising solution to some different artefacts problems especially when it is combined with other techniques, e.g., combining the first derivative and simple spectral ratio can correct both the additive effects and multiplicative effects [25].…”

Section: Pre-processing Techniquesmentioning

confidence: 99%

Current Application of Advancing Spectroscopy Techniques in Food Analysis: Data Handling with Chemometric Approaches

Kharbach,

Alaoui Mansouri,

Taabouz

et al. 2023

Foods

View full text Add to dashboard Cite

In today’s era of increased food consumption, consumers have become more demanding in terms of safety and the quality of products they consume. As a result, food authorities are closely monitoring the food industry to ensure that products meet the required standards of quality. The analysis of food properties encompasses various aspects, including chemical and physical descriptions, sensory assessments, authenticity, traceability, processing, crop production, storage conditions, and microbial and contaminant levels. Traditionally, the analysis of food properties has relied on conventional analytical techniques. However, these methods often involve destructive processes, which are laborious, time-consuming, expensive, and environmentally harmful. In contrast, advanced spectroscopic techniques offer a promising alternative. Spectroscopic methods such as hyperspectral and multispectral imaging, NMR, Raman, IR, UV, visible, fluorescence, and X-ray-based methods provide rapid, non-destructive, cost-effective, and environmentally friendly means of food analysis. Nevertheless, interpreting spectroscopy data, whether in the form of signals (fingerprints) or images, can be complex without the assistance of statistical and innovative chemometric approaches. These approaches involve various steps such as pre-processing, exploratory analysis, variable selection, regression, classification, and data integration. They are essential for extracting relevant information and effectively handling the complexity of spectroscopic data. This review aims to address, discuss, and examine recent studies on advanced spectroscopic techniques and chemometric tools in the context of food product applications and analysis trends. Furthermore, it focuses on the practical aspects of spectral data handling, model construction, data interpretation, and the general utilization of statistical and chemometric methods for both qualitative and quantitative analysis. By exploring the advancements in spectroscopic techniques and their integration with chemometric tools, this review provides valuable insights into the potential applications and future directions of these analytical approaches in the food industry. It emphasizes the importance of efficient data handling, model development, and practical implementation of statistical and chemometric methods in the field of food analysis.

show abstract

Section: Pre-processing Techniquesmentioning

confidence: 99%

Current Application of Advancing Spectroscopy Techniques in Food Analysis: Data Handling with Chemometric Approaches

Kharbach,

Alaoui Mansouri,

Taabouz

et al. 2023

Foods

View full text Add to dashboard Cite

show abstract

“…Global peak picking algorithms have recently been designed to better align dense biological data, providing hope for the field of twodimensional GC-MS for cellular metabolome analyses. 124 Overall, the use of GC-MS analyses provides a unique opportunity to study intracellular metabolism, which could be manipulated for less-invasive diagnostic testing.…”

Section: ■ Commonly Utilized Instrument Platformsmentioning

confidence: 99%

“…Although the technique has promise in the cellular metabolomics space, the ubiquitous use of GC×GC-MS in metabolomics is lacking, primarily due to issues arising during data analysis as a result of the complex data generated. Global peak picking algorithms have recently been designed to better align dense biological data, providing hope for the field of two-dimensional GC-MS for cellular metabolome analyses . Overall, the use of GC-MS analyses provides a unique opportunity to study intracellular metabolism, which could be manipulated for less-invasive diagnostic testing.…”

Section: Commonly Utilized Instrument Platformsmentioning

confidence: 99%

Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions

et al. 2020

View full text Add to dashboard Cite

“…Non-rigid transformation then allows non-uniform scaling and skewing of the data during the transformation. Li et al [ 4 ] developed a spectral similarity extension algorithm for CPD, which should outperform local alignment algorithms in cases of real data with a high density of peaks. One of the most favourite data alignment algorithms is correlation optimized warping algorithm [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

DA_2DCHROM — a data alignment tool for applications on real GC × GC–TOF samples

Ladislavová

Urban

2023

Anal Bioanal Chem

View full text Add to dashboard Cite

Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC–MS) has great potential for analyses of complicated mixtures and sample matrices, due to its separation power and possible high resolution. The second component of the measurement results, the mass spectra, is reproducible. However, the reproducibility of two-dimensional chromatography is affected by many factors and makes the evaluation of long-term experiments or cross-laboratory collaborations complicated. This paper presents a new open-source data alignment tool to tackle the problem of retention time shifts — with 5 different algorithms implemented: BiPACE 2D, DISCO, MSort, PAM, and TNT-DA, along with Pearson’s correlation and dot product as optional methods for mass spectra comparison. The implemented data alignment algorithms and their variations were tested on real samples to demonstrate the functionality of the presented tool. The suitability of each implemented algorithm for significantly/non-significantly shifted data was discussed on the basis of the results obtained. For the evaluation of the “goodness” of the alignment, Kolmogorov–Smirnov test values were calculated, and comparison graphs were generated. The DA_2DChrom is available online with its documentation, fully open-sourced, and the user can use the tool without the need of uploading their data to external third-party servers. Graphical Abstract

show abstract

Coherent point drift peak alignment algorithms using distance and similarity measures for two‐dimensional gas chromatography mass spectrometry data

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as

Cited by 7 publications

References 24 publications

Current Application of Advancing Spectroscopy Techniques in Food Analysis: Data Handling with Chemometric Approaches

Current Application of Advancing Spectroscopy Techniques in Food Analysis: Data Handling with Chemometric Approaches

Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions

DA_2DCHROM — a data alignment tool for applications on real GC × GC–TOF samples

Contact Info

Product

Resources

About