scholarly journals Curatr: a web application for creating, curating, and sharing a mass spectral library

2017 ◽  
Author(s):  
Andrew Palmer ◽  
Prasad Phapale ◽  
Dominik Fay ◽  
Theodore Alexandrov
Keyword(s):  
Mass Spectrometry ◽  
Web Application ◽  
Mass Spectrometry Analysis ◽  
Supplementary Information ◽  
Spectral Library ◽  
Mass Spectral Fragmentation ◽  
Mass Spectral ◽  
Link Type ◽  
Manual Curation

AbstractMotivationIdentification from metabolomics mass spectrometry experiments requires comparison of fragmentation spectra from experimental samples to spectra from analytical standards. As the quality of identification depends directly on the quality of the reference spectra, manual curation is routine during the selection of reference spectra to include in a spectral library. Whilst building our own in-house spectral library we realised that there is currently no vendor neutral open access tool for for facilitating manual curation of spectra from raw LC-MS data into a custom spectral library.ResultsWe developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries for liquid-chromatography mass spectrometry analysis. Curatr handles datasets from single or multiplexed standards, automatically extracting chromatographic profiles and potential fragmentation spectra for multiple adducts. These are presented through an intuitive interface for manual curation before being documented in a custom spectral library. Searchable molecular information and the providence of each standard is stored along with metadata on the experimental protocol. Curatr support the export of spectral libraries in several standard formats for easy use with third party software or submission to community databases, maximising the return on investment for these costly measurements. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library which is publicly available at http://curatr.mcf.embl.de.AvailabilityThe source code is freely available at http://github.com/alexandrovteam/curatr/ along with example data.Supplementary informationA step-by step user manual is available in the supplementary information

scholarly journals N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zhiwu An ◽  
Qingbo Shu ◽  
Hao Lv ◽  
Lian Shu ◽  
Jifeng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Peptide Identification ◽  
High Energy ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

scholarly journals PathScore: a web tool for identifying altered pathways in cancer data

2016 ◽  
Author(s):  
Stephen G. Gaffney ◽  
Jeffrey P. Townsend
Keyword(s):  
Web Application ◽  
Somatic Mutations ◽  
Supplementary Information ◽  
Web Tool ◽  
Cancer Data ◽  
Link Type ◽  
Novel Approach ◽  
Supplementary Material ◽  
User Friendly ◽  
Pathway Effect

ABSTRACTSummaryPathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.Availability and ImplementationWeb application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at github.com/sggaffney/pathscore with a GPLv3 [email protected] InformationAdditional documentation can be found at http://pathscore.publichealth.yale.edu/faq.

Massenspektrometrische Fragmentierung von Trimethylsilylderivaten (TMS) des Thyrotropin-„Releasing“-Hormons (TRH) und dessen Teilstrukturen / Mass Spectroscopy of Trimethylsilyl Derivatives of Thyrotropin-releasing Hormone and its Constituents

1973 ◽  
Vol 28 (11-12) ◽  
pp. 820-823 ◽  
Author(s):  
W. A. König ◽  
S. Fuchs ◽  
K. Zech ◽  
W. Voelter
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectroscopy ◽  
Peptide Hormones ◽  
Thyrotropin Releasing Hormone ◽  
Mass Spectral Fragmentation ◽  
Releasing Hormone ◽  
Mass Spectral ◽  
Trimethylsilyl Derivatives ◽  
Fragmentation Patterns ◽  
Derivatives Of

The mass spectral fragmentation patterns of trimethylsilyl derivatives of TRH and its constituents are discussed. The utility of these derivatives for the control of the synthesis of peptide hormones by mass spectrometry is obvious.

scholarly journals Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library

2017 ◽  
Vol 55 (10) ◽  
pp. 2924-2933 ◽  
Author(s):  
Laurence Lachaud ◽  
Anna Fernández-Arévalo ◽  
Anne-Cécile Normand ◽  
Patrick Lami ◽  
Cécile Nabet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Leishmania Donovani ◽  
Identification System ◽  
Enzyme Electrophoresis ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Web Based ◽  
Content Type ◽  
Mass Spectral ◽  
Scalable Database

ABSTRACT Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania . However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani , L. guyanensis , and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers.

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