MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

Data Dependent Peak Model Based Spectrum Deconvolution for Analysis of High Resolution LC-MS Data

A data dependent peak model (DDPM) based spectrum deconvolution method was developed for analysis of high resolution LC-MS data. To construct the selected ion chromatogram (XIC), a clustering method, the density based spatial clustering of applications with noise (DBSCAN), is applied to all m/z values of an LC-MS data set to group the m/z values into each XIC. The DBSCAN constructs XICs without...

Contrasts, Independent Component Analysis, and Blind Deconvolution

DIANA - algorithmic improvements for analysis of data-independent acquisition MS data

MOTIVATION Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide qualit...

A tool for the automated, targeted analysis of data-independent acquisition MS-data: OpenSWATH

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users reco...

PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data

Summary The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis from mass spectrometry data acquisition to biological interpretation. Our key innovations are the Summary Page, which provides a simple overview of the experiment in the format of a scientific paper, containing the key findings of th...