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

2018 ◽  
Vol 17 (6) ◽  
pp. 1239-1244 ◽  
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.

High field FT-ICR mass spectrometry data sets enlighten qualitative DOM alteration in lake sediment porewater profiles

2017 ◽  
Vol 108 ◽  
pp. 51-60 ◽  
Author(s):  
Peter Herzsprung ◽  
Wolf von Tümpling ◽  
Katrin Wendt-Potthoff ◽  
Norbert Hertkorn ◽  
Mourad Harir ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Lake Sediment ◽  
High Field ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Ft Icr

scholarly journals mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets

2011 ◽  
Vol 11 (1) ◽  
pp. O111.011379 ◽  
Author(s):  
Mathias Wilhelm ◽  
Marc Kirchner ◽  
Judith A. J. Steen ◽  
Hanno Steen
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Space And Time ◽  
Efficient Storage

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

2020 ◽  
Author(s):  
Thibault Robin ◽  
Julien Mariethoz ◽  
Frédérique Lisacek
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Web Application ◽  
Contextual Information ◽  
Fine Tuning ◽  
Data Sources ◽  
Mass Spectrometry Data ◽  
Web Interface ◽  
Definition Of ◽  
Selection Of

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.

scholarly journals A Bi-directional Hierarchical Clustering (BHC) for Peak Matching of Large Mass Spectrometry Data Sets

2021 ◽  
Vol 11 (6) ◽  
pp. 373-379
Author(s):  
Nazanin Zounemat Kermani ◽  
◽  
Xian Yang ◽  
Yike Guo ◽  
James McKenzie ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Hierarchical Clustering ◽  
Large Mass ◽  
Mass Spectrometry Data ◽  
Data Sets

scholarly journals Dereplikace látek a de novo charakterizace malých molekul z hmotnostních spekter

2022 ◽  
Vol 116 (1) ◽  
pp. 11-19
Author(s):  
Jiří Novák ◽  
Vladimír Havlíček
Keyword(s):  
Mass Spectrometry ◽  
Small Molecules ◽  
Mass Spectra ◽  
De Novo ◽  
Imaging Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Liquid Chromatography Mass Spectrometry ◽  
Imaging Mass Spectrometry Data

We describe the molecular dereplication principles and de novo characterization of small molecules obtained from liquid-chromatography mass spectrometry and imaging mass spectrometry data sets. Our methodology aims at supporting chemists and computer programmers to understand the hidden computing algorithms used for metabolomics mass spectrometry data processing. The approaches have been made available in the open-source tool CycloBranch. The presented tutorial extends the interpretation of mass spectra portfolia described in a series of papers published in Chemicke Listy, issues 2/2020 and 3/2020.

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