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Literature DB >> 24174567

MSPrep--summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data.

Grant Hughes¹, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina Kechris.

Abstract

MOTIVATION: Although R packages exist for the pre-processing of metabolomic data, they currently do not incorporate additional analysis steps of summarization, filtering and normalization of aligned data. We developed the MSPrep R package to complement other packages by providing these additional steps, implementing a selection of popular normalization algorithms and generating diagnostics to help guide investigators in their analyses. AVAILABILITY: http://www.sourceforge.net/projects/msprep

Mesh：

Year: 2013 PMID： 24174567 PMCID： PMC3866554 DOI： 10.1093/bioinformatics/btt589

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

13 in total

1. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards.

Authors: Weixun Wang; Haihong Zhou; Hua Lin; Sushmita Roy; Thomas A Shaler; Lander R Hill; Scott Norton; Praveen Kumar; Markus Anderle; Christopher H Becker
Journal: Anal Chem Date: 2003-09-15 Impact factor: 6.986

2. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors: B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal: Bioinformatics Date: 2003-01-22 Impact factor: 6.937

3. A Bayesian missing value estimation method for gene expression profile data.

Authors: Shigeyuki Oba; Masa-aki Sato; Ichiro Takemasa; Morito Monden; Ken-ichi Matsubara; Shin Ishii
Journal: Bioinformatics Date: 2003-11-01 Impact factor: 6.937

4. Using control genes to correct for unwanted variation in microarray data.

Authors: Johann A Gagnon-Bartsch; Terence P Speed
Journal: Biostatistics Date: 2011-11-17 Impact factor: 5.899

5. Adjusting batch effects in microarray expression data using empirical Bayes methods.

Authors: W Evan Johnson; Cheng Li; Ariel Rabinovic
Journal: Biostatistics Date: 2006-04-21 Impact factor: 5.899

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

Authors: Colin A Smith; Elizabeth J Want; Grace O'Maille; Ruben Abagyan; Gary Siuzdak
Journal: Anal Chem Date: 2006-02-01 Impact factor: 6.986

7. pcaMethods--a bioconductor package providing PCA methods for incomplete data.

Authors: Wolfram Stacklies; Henning Redestig; Matthias Scholz; Dirk Walther; Joachim Selbig
Journal: Bioinformatics Date: 2007-03-07 Impact factor: 6.937

8. Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data.

Authors: Henning Redestig; Atsushi Fukushima; Hans Stenlund; Thomas Moritz; Masanori Arita; Kazuki Saito; Miyako Kusano
Journal: Anal Chem Date: 2009-10-01 Impact factor: 6.986

9. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.

Authors: Tomás Pluskal; Sandra Castillo; Alejandro Villar-Briones; Matej Oresic
Journal: BMC Bioinformatics Date: 2010-07-23 Impact factor: 3.169

10. xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

Authors: Karan Uppal; Quinlyn A Soltow; Frederick H Strobel; W Stephen Pittard; Kim M Gernert; Tianwei Yu; Dean P Jones
Journal: BMC Bioinformatics Date: 2013-01-16 Impact factor: 3.169

27 in total

1. The discordant method: a novel approach for differential correlation.

Authors: Charlotte Siska; Russell Bowler; Katerina Kechris
Journal: Bioinformatics Date: 2015-10-31 Impact factor: 6.937

2. Pre-analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data.

Authors: Dominik Reinhold; Harrison Pielke-Lombardo; Sean Jacobson; Debashis Ghosh; Katerina Kechris
Journal: Methods Mol Biol Date: 2019

3. Early Mechanistic Events Induced by Low Molecular Weight Polycyclic Aromatic Hydrocarbons in Mouse Lung Epithelial Cells: A Role for Eicosanoid Signaling.

Authors: Katelyn J Siegrist; DeeDee Romo; Brad L Upham; Michael Armstrong; Kevin Quinn; Lauren Vanderlinden; Ross S Osgood; Kalpana Velmurugan; Marc Elie; Jonathan Manke; Dominik Reinhold; Nichole Reisdorph; Laura Saba; Alison K Bauer
Journal: Toxicol Sci Date: 2019-05-01 Impact factor: 4.849

Review 4. Computational Metabolomics: A Framework for the Million Metabolome.

Authors: Karan Uppal; Douglas I Walker; Ken Liu; Shuzhao Li; Young-Mi Go; Dean P Jones
Journal: Chem Res Toxicol Date: 2016-10-12 Impact factor: 3.739

5. Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans.

Authors: Christopher M Depner; Dasha T Cogswell; Paul J Bisesi; Rachel R Markwald; Charmion Cruickshank-Quinn; Kevin Quinn; Edward L Melanson; Nichole Reisdorph; Kenneth P Wright
Journal: Sleep Date: 2020-07-13 Impact factor: 5.849

6. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules.

Authors: Lucas A Gillenwater; Katherine A Pratte; Brian D Hobbs; Michael H Cho; Yonghua Zhuang; Eitan Halper-Stromberg; Charmion Cruickshank-Quinn; Nichole Reisdorph; Irina Petrache; Wassim W Labaki; Wanda K O'Neal; Victor E Ortega; Dean P Jones; Karan Uppal; Sean Jacobson; Gregory Michelotti; Christine H Wendt; Katerina J Kechris; Russell P Bowler
Journal: Netw Syst Med Date: 2020-12-31