Dataset Information

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

ABSTRACT: We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes. It is applied here to reveal systemic proteoform variations in the yeast response to salt stress.

SUBMITTER: Cesnik AJ

PROVIDER: S-EPMC5770237 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Cesnik Anthony J AJ Shortreed Michael R MR Schaffer Leah V LV Knoener Rachel A RA Frey Brian L BL Scalf Mark M Solntsev Stefan K SK Dai Yunxiang Y Gasch Audrey P AP Smith Lloyd M LM

Journal of proteome research 20171215 1

We present an open-source, interactive program named Proteoform Suite that uses proteoform mass and intensity measurements from complex biological samples to identify and quantify proteoforms. It constructs families of proteoforms derived from the same gene, assesses proteoform function using gene ontology (GO) analysis, and enables visualization of quantified proteoform families and their changes. It is applied here to reveal systemic proteoform variations in the yeast response to salt stress. ...[more]

PMID: 29195273

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Project description:BackgroundGastrointestinal contractions are controlled by an underlying bioelectrical activity. High-resolution spatiotemporal electrical mapping has become an important advance for investigating gastrointestinal electrical behaviors in health and motility disorders. However, research progress has been constrained by the low efficiency of the data analysis tasks. This work introduces a new efficient software package: GEMS (Gastrointestinal Electrical Mapping Suite), for analyzing and visualizing high-resolution multi-electrode gastrointestinal mapping data in spatiotemporal detail.ResultsGEMS incorporates a number of new and previously validated automated analytical and visualization methods into a coherent framework coupled to an intuitive and user-friendly graphical user interface. GEMS is implemented using MATLAB®, which combines sophisticated mathematical operations and GUI compatibility. Recorded slow wave data can be filtered via a range of inbuilt techniques, efficiently analyzed via automated event-detection and cycle clustering algorithms, and high quality isochronal activation maps, velocity field maps, amplitude maps, frequency (time interval) maps and data animations can be rapidly generated. Normal and dysrhythmic activities can be analyzed, including initiation and conduction abnormalities. The software is distributed free to academics via a community user website and forum (http://sites.google.com/site/gimappingsuite).ConclusionsThis software allows for the rapid analysis and generation of critical results from gastrointestinal high-resolution electrical mapping data, including quantitative analysis and graphical outputs for qualitative analysis. The software is designed to be used by non-experts in data and signal processing, and is intended to be used by clinical researchers as well as physiologists and bioengineers. The use and distribution of this software package will greatly accelerate efforts to improve the understanding of the causes and clinical consequences of gastrointestinal electrical disorders, through high-resolution electrical mapping.

Dataset Information

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Publications

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Similar Datasets

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