scholarly journals GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

2020 ◽  
Vol 16 ◽  
pp. 2127-2135 ◽  
Author(s):  
Toan K Phung ◽  
Cassandra L Pegg ◽  
Benjamin L Schulz
Keyword(s):  
Mass Spectrometry ◽  
Hepatocellular Carcinoma ◽  
Data Analysis ◽  
High Throughput ◽  
Protein Glycosylation ◽  
Software Pipeline ◽  
Site Specific ◽  
Proteome Discoverer ◽  
Automated Software

Mass spectrometry glycoproteomics is rapidly maturing, allowing unprecedented insights into the diversity and functions of protein glycosylation. However, quantitative glycoproteomics remains challenging. We developed GlypNirO, an automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis. The output of GlypNirO is clearly structured, allowing manual interrogation, and is also appropriate for input into diverse statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease.

scholarly journals GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

2020 ◽  
Author(s):  
Toan K. Phung ◽  
Cassandra L. Pegg ◽  
Benjamin L. Schulz
Keyword(s):  
Mass Spectrometry ◽  
Hepatocellular Carcinoma ◽  
Data Analysis ◽  
High Throughput ◽  
Protein Glycosylation ◽  
Software Pipeline ◽  
Site Specific ◽  
Proteome Discoverer ◽  
Automated Software

AbstractMass spectrometry glycoproteomics is rapidly maturing, allowing unprecedented insights into the diversity and functions of protein glycosylation. However, quantitative glycoproteomics remains challenging. We developed GlypNirO, an automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis. The output of GlypNirO is clearly structured, allowing manual interrogation, and is also appropriate for input into diverse statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease.

scholarly journals Global and site‐specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry

2019 ◽  
Vol 38 (4-5) ◽  
pp. 356-379 ◽  
Author(s):  
Haopeng Xiao ◽  
Fangxu Sun ◽  
Suttipong Suttapitugsakul ◽  
Ronghu Wu
Keyword(s):  
Mass Spectrometry ◽  
Biological Systems ◽  
Protein Glycosylation ◽  
Site Specific ◽  
Specific Analysis

High-Throughput Data Analysis of Proteomic Mass Spectra on the SwissBioGrid

2011 ◽  
pp. 228-244
Author(s):  
Andreas Quandt ◽  
Sergio Maffioletti ◽  
Cesare Pautasso ◽  
Heinz Stockinger ◽  
Frederique Lisacek
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
High Throughput ◽  
Protein Function ◽  
Mass Spectra ◽  
High Throughput Data ◽  
Analysis Process ◽  
Speed Up ◽  
Grid Infrastructures ◽  
High Throughput Data Analysis

Proteomics is currently one of the most promising fields in bioinformatics as it provides important insights into the protein function of organisms. Mass spectrometry is one of the techniques to study the proteome, and several software tools exist for this purpose. The authors provide an extendable software platform called swissPIT that combines different existing tools and exploits Grid infrastructures to speed up the data analysis process for the proteomics pipeline.

scholarly journals Sensitive and fast characterization of site-specific protein glycosylation with capillary electrophoresis coupled to mass spectrometry

Talanta ◽  
2018 ◽  
Vol 179 ◽  
pp. 22-27 ◽  
Author(s):  
Yanyan Qu ◽  
Liangliang Sun ◽  
Guijie Zhu ◽  
Zhenbin Zhang ◽  
Elizabeth H. Peuchen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Capillary Electrophoresis ◽  
Specific Protein ◽  
Protein Glycosylation ◽  
Site Specific

scholarly journals At-line high throughput site-specific glycan profiling using targeted mass spectrometry

2020 ◽  
Vol 25 ◽  
pp. e00424
Author(s):  
Bertie Chi ◽  
Christel Veyssier ◽  
Toyin Kasali ◽  
Faisal Uddin ◽  
Christopher A. Sellick
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Site Specific ◽  
Glycan Profiling

scholarly journals Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics

Proteomes ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 15
Author(s):  
Benjamin C. Orsburn
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Tandem Mass Spectrometry ◽  
Data Processing ◽  
Recent History ◽  
Tandem Mass ◽  
Central Theme ◽  
Initial Release ◽  
Proteome Discoverer

Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today.

PepLine: A Software Pipeline for High-Throughput Direct Mapping of Tandem Mass Spectrometry Data on Genomic Sequences

2008 ◽  
Vol 7 (5) ◽  
pp. 1873-1883 ◽  
Author(s):  
Myriam Ferro ◽  
Marianne Tardif ◽  
Erwan Reguer ◽  
Romain Cahuzac ◽  
Christophe Bruley ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data ◽  
Genomic Sequences ◽  
Tandem Mass ◽  
Software Pipeline ◽  
Direct Mapping ◽  
Tandem Mass Spectrometry Data
Sign in / Sign up

Export Citation Format

Share Document