An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

LN Mueller, MY Brusniak, DR Mani… - Journal of proteome …, 2008 - ACS Publications
Over the past decade, a series of experimental strategies for mass spectrometry based
quantitative proteomics and corresponding computational methodology for the processing of …

Data processing for mass spectrometry-based metabolomics

M Katajamaa, M Orešič - Journal of chromatography A, 2007 - Elsevier
Modern analytical technologies afford comprehensive and quantitative investigation of a
multitude of different metabolites. Typical metabolomic experiments can therefore produce …

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

M Gulia-Nuss, AB Nuss, JM Meyer… - Nature …, 2016 - nature.com
Ticks transmit more pathogens to humans and animals than any other arthropod. We
describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors …

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

K Uppal, QA Soltow, FH Strobel, WS Pittard… - BMC …, 2013 - Springer
Background Detection of low abundance metabolites is important for de novo map** of
metabolic pathways related to diet, microbiome or environmental exposures. Multiple …

Normalization strategies for metabonomic analysis of urine samples

BM Warrack, S Hnatyshyn, KH Ott, MD Reily… - … of Chromatography B, 2009 - Elsevier
Unlike plasma and most biological fluids which have solute concentrations that are tightly
controlled, urine volume can vary widely based upon water consumption and other …

Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery

KA Veselkov, LK Vingara, P Masson… - Analytical …, 2011 - ACS Publications
Ultra-performance liquid chromatography coupled to mass spectrometry (UPLC/MS) has
been used increasingly for measuring changes of low molecular weight metabolites in …

Analysis of immunoglobulin glycosylation by LC‐ESI‐MS of glycopeptides and oligosaccharides

J Stadlmann, M Pabst, D Kolarich, R Kunert… - …, 2008 - Wiley Online Library
Abstract Two LC‐ESI‐MS methods for the analysis of antibody glycosylation are presented.
In the first approach, tryptic glycopeptides are separated by RP chromatography and …

Algorithms and tools for the preprocessing of LC–MS metabolomics data

S Castillo, P Gopalacharyulu, L Yetukuri… - … and Intelligent Laboratory …, 2011 - Elsevier
Metabolomics encompasses the study of small molecules in a biological sample. Liquid
Chromatography coupled with Mass Spectrometry (LC–MS) profiling is an important …

LC-MS alignment in theory and practice: a comprehensive algorithmic review

R Smith, D Ventura, JT Prince - Briefings in bioinformatics, 2015 - academic.oup.com
Liquid chromatography-mass spectrometry is widely used for comparative replicate sample
analysis in proteomics, lipidomics and metabolomics. Before statistical comparison …

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

E Lange, R Tautenhahn, S Neumann, C Gröpl - BMC bioinformatics, 2008 - Springer
Background Liquid chromatography coupled to mass spectrometry (LC-MS) has become a
prominent tool for the analysis of complex proteomics and metabolomics samples. In many …