Examining and fine-tuning the selection of glycan compositions with GlyConnect Compozitor

AbstractA key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing mass spectrometry data. We introduce here a glycan composition visualising and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor. It has web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted at https://glyconnect.expasy.org/compozitor/ where it can be run as a web application. It is also directly accessible from the GlyConnect database.

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Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor

Molecular & Cellular Proteomics ◽

10.1074/mcp.ra120.002041 ◽

2020 ◽

Vol 19 (10) ◽

pp. 1602-1618 ◽

Cited By ~ 1

Author(s):

Thibault Robin ◽

Julien Mariethoz ◽

Frédérique Lisacek

Keyword(s):

Search Engine ◽

Posttranslational Modifications ◽

Search Engines ◽

Web Application ◽

Contextual Information ◽

Fine Tuning ◽

Data Sources ◽

Web Interface ◽

Definition Of ◽

Selection Of

A key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing MS data. We introduce here a glycan composition visualizing and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor. It offers a web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarizing information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. They also confirm the consistency of a set of compositions based on the content of the GlyConnect database. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted at https://glyconnect.expasy.org/compozitor/ where it can be run as a web application. It is also directly accessible from the GlyConnect database.

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Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS

Bioinformatics and Biology Insights ◽

10.1177/1177932219868223 ◽

2019 ◽

Vol 13 ◽

pp. 117793221986822 ◽

Cited By ~ 3

Author(s):

Jean Lesne ◽

Marie-Pierre Bousquet ◽

Julien Marcoux ◽

Marie Locard-Paulet

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Data Visualization ◽

Web Application ◽

Three Dimensional ◽

Mass Spectrometry Data ◽

Intact Protein ◽

Top Down ◽

Molecular Weights ◽

Protein Mass

The rise of intact protein analysis by mass spectrometry (MS) was accompanied by an increasing need for flexible tools allowing data visualization and analysis. These include inspection of the deconvoluted molecular weights of the proteoforms eluted alongside liquid chromatography (LC) through their representation in three-dimensional (3D) liquid chromatography coupled to mass spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention times, and intensity of the MS signal). With this aim, we developed a free and open-source web application named VisioProt-MS ( https://masstools.ipbs.fr/mstools/visioprot-ms/ ). VisioProt-MS is highly compatible with many algorithms and software developed by the community to integrate and deconvolute top-down and intact protein MS data. Its dynamic and user-friendly features greatly facilitate analysis through several graphical representations dedicated to MS and tandem mass spectrometry (MS/MS) analysis of proteoforms in complex samples. Here, we will illustrate the importance of LC-MS map visualization to optimize top-down acquisition/search parameters and analyze intact protein MS data. We will go through the main features of VisioProt-MS using the human proteasomal 20S core particle as a user-case.

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Spotlite: Web Application and Augmented Algorithms for Predicting Co-Complexed Proteins from Affinity Purification – Mass Spectrometry Data

Journal of Proteome Research ◽

10.1021/pr5008416 ◽

2014 ◽

Vol 13 (12) ◽

pp. 5944-5955 ◽

Cited By ~ 14

Author(s):

Dennis Goldfarb ◽

Bridgid E. Hast ◽

Wei Wang ◽

Michael B. Major

Keyword(s):

Mass Spectrometry ◽

Web Application ◽

Affinity Purification ◽

Mass Spectrometry Data ◽

Affinity Purification Mass Spectrometry

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Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline

Molecular & Cellular Proteomics ◽

10.1074/mcp.ra117.000543 ◽

2018 ◽

Vol 17 (6) ◽

pp. 1239-1244 ◽

Cited By ~ 55

Author(s):

Vagisha Sharma ◽

Josh Eckels ◽

Birgit Schilling ◽

Christina Ludwig ◽

Jacob D. Jaffe ◽

...

Keyword(s):

Mass Spectrometry ◽

Web Application ◽

Mass Spectrometry Data ◽

Data Management System ◽

Data Sets ◽

Public Repository ◽

Full Data ◽

Manuscript Review ◽

Open Source Data ◽

Chromatographic Peaks

To address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers and readers immediate visual access to the data behind published conclusions, we present Panorama Public (https://panoramaweb.org/public.url), a repository of Skyline documents supporting published results. Panorama Public is built on Panorama, an open source data management system for mass spectrometry data processed with the Skyline targeted mass spectrometry environment. The Panorama web application facilitates viewing, sharing, and disseminating results contained in Skyline documents via a web-browser. Skyline users can easily upload their documents to a Panorama server and allow other researchers to explore uploaded results in the Panorama web-interface through a variety of familiar summary graphs as well as annotated views of the chromatographic peaks processed with Skyline. This makes Panorama ideal for sharing targeted, quantitative results contained in Skyline documents with collaborators, reviewers, and the larger proteomics community. The Panorama Public repository employs the full data visualization capabilities of Panorama which facilitates sharing results with reviewers during manuscript review.

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A Cautionary Tale on the Inclusion of Variable Posttranslational Modifications in Database-Dependent Searches of Mass Spectrometry Data

Methods in Enzymology - Proteomics in Biology, Part B ◽

10.1016/bs.mie.2016.11.007 ◽

2017 ◽

pp. 433-452 ◽

Cited By ~ 7

Author(s):

J. Svozil ◽

K. Baerenfaller

Keyword(s):

Mass Spectrometry ◽

Posttranslational Modifications ◽

Mass Spectrometry Data ◽

Cautionary Tale

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Pipeline of Mass-spectrometry Data Processing for Diagnostic Molecular Marker Panel Obtaining Using the Example of Search Markers of Breast Cancer Metastasis

Biomedical Chemistry Research and Methods ◽

10.18097/bmcrm00156 ◽

2021 ◽

Vol 4 (3) ◽

pp. e00156

Author(s):

A.O. Tokareva ◽

V.V. Chagovets ◽

A.S. Kononikhin ◽

N.L. Starodubtseva ◽

V.E. Frankevich ◽

...

Keyword(s):

Mass Spectrometry ◽

Molecular Marker ◽

Data Processing ◽

Breast Tissue ◽

Cancer Metastasis ◽

Clinical Medicine ◽

Mass Spectrometry Data ◽

Diagnostic Model ◽

Tissue Samples ◽

Selection Of

A pathology diagnostic using molecular marker is a perspective direction of clinical medicine. Mass-spectrometry (MS) is a one of methods, which are used for obtaining information about molecular profiles. Selection of species, essential for classification “case/control is an important task for data processing. Pipeline of data processing has been proposed using MS data, obtained during analysis of tumor breast tissue samples and health breast tissue samples, with the aim of metastasis marker selection. As a result, selection of lipid markers that belong to classes, related to metastasis and proliferation processes, makes it possible to create high sensitivity diagnostic model, based on logistic regression. The proposed method is applicable for data processing, obtained by MS analysis of other “omics”: metabolome, proteome, glycome.

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Constellation: An Open-Source Web Application for Unsupervised Systematic Trend Detection in High-Resolution Mass Spectrometry Data

Journal of the American Society for Mass Spectrometry ◽

10.1021/jasms.1c00371 ◽

2022 ◽

Author(s):

Dane R. Letourneau ◽

Dietrich A. Volmer

Keyword(s):

Mass Spectrometry ◽

High Resolution ◽

Open Source ◽

Web Application ◽

High Resolution Mass Spectrometry ◽

Mass Spectrometry Data ◽

Trend Detection ◽

Systematic Trend ◽

High Resolution Mass ◽

Resolution Mass

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Configurable Web Warehouses construction through BPM Systems

CLEI electronic journal ◽

10.19153/cleiej.19.2.8 ◽

2016 ◽

Author(s):

Andrea Delgado ◽

Adriana Marotta

Keyword(s):

Business Process Management ◽

Process Management ◽

Business Processes ◽

Data Sources ◽

Proof Of Concept ◽

Business People ◽

Feeding Process ◽

Definition Of ◽

The Web ◽

Selection Of

The process of building Data Warehouses (DW) is well known with well defined stages but at the same time, mostly carried out manually by IT people in conjunction with business people. Web Warehouses (WW) are DW whose data sources are taken from the web. We define a flexible WW, which can be configured accordingly to different domains, through the selection of the web sources and the definition of data processing characteristics. A Business Process Management (BPM) System allows modeling and executing Business Processes (BPs) providing support for the automation of processes. To support the process of building flexible WW we propose a two BPs level: a configuration process to support the selection of web sources and the definition of schemas and mappings, and a feeding process which takes the defined configuration and loads the data into the WW. In this paper we present a proof of concept of both processes, with focus on the configuration process and the defined data.

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Selection and Preparation of Specific Tissue Regions For Tem Using Large Epoxy-Embedded Blocks

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007206x ◽

1973 ◽

Vol 31 ◽

pp. 324-325 ◽

Cited By ~ 1

Author(s):

P. M. Lowrie ◽

W. S. Tyler

Keyword(s):

Electron Microscopy ◽

Anatomical Structures ◽

Ultrastructural Studies ◽

Transmission Electron ◽

Microscopic Evaluation ◽

Embedded Blocks ◽

Specific Tissue ◽

Definition Of ◽

Areas Of Interest ◽

Selection Of

The importance of examining stained 1 to 2μ plastic sections by light microscopy has long been recognized, both for increased definition of many histologic features and for selection of specimen samples to be used in ultrastructural studies. Selection of specimens with specific orien ation relative to anatomical structures becomes of critical importance in ultrastructural investigations of organs such as the lung. The uantity of blocks necessary to locate special areas of interest by random sampling is large, however, and the method is lacking in precision. Several methods have been described for selection of specific areas for electron microscopy using light microscopic evaluation of paraffin, epoxy-infiltrated, or epoxy-embedded large blocks from which thick sections were cut. Selected areas from these thick sections were subsequently removed and re-embedded or attached to blank precasted blocks and resectioned for transmission electron microscopy (TEM).

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