Bioinformatics methods for mass spectrometry-based proteomics data analysis

C Chen, J Hou, JJ Tanner, J Cheng - International journal of molecular …, 2020 - mdpi.com
Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous
progress in the understanding of cellular mechanisms, disease progression, and the …

High resolution mass spectrometry in lipidomics

T Züllig, HC Köfeler - Mass spectrometry reviews, 2021 - Wiley Online Library
The boost of research output in lipidomics during the last decade is tightly linked to improved
instrumentation in mass spectrometry. Associated with this trend is the shift from low …

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Z Pang, J Chong, G Zhou… - Nucleic acids …, 2021 - academic.oup.com
Since its first release over a decade ago, the MetaboAnalyst web-based platform has
become widely used for comprehensive metabolomics data analysis and interpretation …

MetaboAnalystR 3.0: toward an optimized workflow for global metabolomics

Z Pang, J Chong, S Li, J Xia - Metabolites, 2020 - mdpi.com
Liquid chromatography coupled to high-resolution mass spectrometry platforms are
increasingly employed to comprehensively measure metabolome changes in systems …

NOREVA: normalization and evaluation of MS-based metabolomics data

B Li, J Tang, Q Yang, S Li, X Cui, Y Li… - Nucleic acids …, 2017 - academic.oup.com
Diverse forms of unwanted signal variations in mass spectrometry-based metabolomics data
adversely affect the accuracies of metabolic profiling. A variety of normalization methods …

A systematic evaluation of normalization methods in quantitative label-free proteomics

T Välikangas, T Suomi, LL Elo - Briefings in bioinformatics, 2018 - academic.oup.com
To date, mass spectrometry (MS) data remain inherently biased as a result of reasons
ranging from sample handling to differences caused by the instrumentation. Normalization is …

Systematic error removal using random forest for normalizing large-scale untargeted lipidomics data

S Fan, T Kind, T Cajka, SL Hazen, WHW Tang… - Analytical …, 2019 - ACS Publications
Large-scale untargeted lipidomics experiments involve the measurement of hundreds to
thousands of samples. Such data sets are usually acquired on one instrument over days or …

Navigating freely-available software tools for metabolomics analysis

R Spicer, RM Salek, P Moreno, D Cañueto… - Metabolomics, 2017 - Springer
Introduction The field of metabolomics has expanded greatly over the past two decades,
both as an experimental science with applications in many areas, as well as in regards to …

NormalyzerDE: online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis

J Willforss, A Chawade, F Levander - Journal of proteome …, 2018 - ACS Publications
Technical biases are introduced in omics data sets during data generation and interfere with
the ability to study biological mechanisms. Several normalization approaches have been …

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine

AH Emwas, E Saccenti, X Gao, RT McKay… - Metabolomics, 2018 - Springer
Abstract 1 H NMR spectra from urine can yield information-rich data sets that offer important
insights into many biological and biochemical phenomena. However, the quality and utility …