GNPS - Living Data - Continuous Identification - Networks and Identification Dump
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Various
ORGANISM(S): Various
SUBMITTER: 
Mingxun Wang
PROVIDER: MSV000084314 | GNPS |
REPOSITORIES: GNPS
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Project description:Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching.
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Project description:The establishment of a high-quality mouse brain transmembrane proteins spectral library enables in-depth profiling of the proteins across multiple brain regions. DIA data analysis, combining different search pipeline based on the spectral library, discovered a new GPCR regulator which was associated with depression verified via in vivo tests. This library represents a valuable resource that has the potential to discover the putative drug targets.
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Project description:In order to assess the quality of alleged PM identifications from Arabidopsis, PM-enriched fractions were compared to PM-depleted fractions using 18O isotopic labeling and mass spectrometry. The two samples submitted are biological replicates. Keywords: Protein Localization via MS
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Project description:<p>Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics studies require high-quality spectral libraries for reliable metabolite identification. We have constructed EMBL-MCF (European Molecular Biology Laboratory-Metabolomics Core Facility), an open LC-MS/MS spectral library that currently contains over 1600 fragmentation spectra from 435 authentic standards of endogenous metabolites and lipids. The unique features of the library include the presence of chromatographic profiles acquired with different LC-MS methods and coverage of different adduct ions. The library covers many biologically important metabolites with some unique metabolites and lipids as compared with other public libraries. The EMBL-MCF spectral library is created and shared using an in-house-developed web application at https://curatr.mcf.embl.de/. The library is freely available online and also integrated with other mass spectral repositories.</p>
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Project description:Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analysis is the availability of spectral libraries for the peptide identification and quantification. Several researches were already conducted regarding the creation of spectral libraries from DDA analyses and obtaining identifications with these in DIA measurements. But so far only few experiments were conducted, to estimate the effect of these libraries on the quantitative level. In this work we created a spike-in gold standard dataset with known contents and ratios of proteins in a complex sample matrix. With this dataset, we first created spectral libraries using different sample preparation approaches with and without sample prefractionation on peptide and protein level. Two different search engines were used for protein identification. In total, five different spike-in states were compared with DIA analyses, comparing eight different spectral libraries generated by varying approaches and one library free method, as well as one default DDA analysis. Not only the number of identifications on peptide and protein level in the spectral libraries and the corresponding analyses was inspected, but also the number of expected and identified significant quantifications and their ratios were thoroughly examined. We found, that while libraries of prefractionationed samples are generally larger, the actually yielded identifications are not increased compared to repetitive non-fractionated measurements. Furthermore, we show that the accuracy of the quantifications is also highly dependent on the applied spectra library and also whether the peptide or protein level is analysed. Overall, the reproducibility and accuracy of DIA is superior to DDA in all analysed approaches.
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Project description:Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analysis is the availability of spectral libraries for the peptide identification and quantification. Several researches were already conducted regarding the creation of spectral libraries from DDA analyses and obtaining identifications with these in DIA measurements. But so far only few experiments were conducted, to estimate the effect of these libraries on the quantitative level. In this work we created a spike-in gold standard dataset with known contents and ratios of proteins in a complex sample matrix. With this dataset, we first created spectral libraries using different sample preparation approaches with and without sample prefractionation on peptide and protein level. Two different search engines were used for protein identification. In total, five different spike-in states were compared with DIA analyses, comparing eight different spectral libraries generated by varying approaches and one library free method, as well as one default DDA analysis. Not only the number of identifications on peptide and protein level in the spectral libraries and the corresponding analyses was inspected, but also the number of expected and identified significant quantifications and their ratios were thoroughly examined. We found, that while libraries of prefractionationed samples are generally larger, the actually yielded identifications are not increased compared to repetitive non-fractionated measurements. Furthermore, we show that the accuracy of the quantifications is also highly dependent on the applied spectra library and also whether the peptide or protein level is analysed. Overall, the reproducibility and accuracy of DIA is superior to DDA in all analysed approaches.
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Project description:Abstract Here we present IPSA, an innovative web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. A tool for the scientific community, IPSA can visualize peptides collected using a wide variety of experimental and instrumental configurations. Annotated spectra are customizable via a selection of interactive features and can be exported as editable scalable vector graphics to aid in the production of publication-quality figures. Single spectra can be analyzed through provided forms, while multiple peptide spectral matches can be uploaded directly to the server as CSV, MGF, or mzML files. IPSA facilitates the characterization of experimental MS/MS performance through the optional export of fragment ion statistics from one to many peptide spectral matches. This resource is made freely accessible at http://interactivepeptidespectralannotator.com, and the source code is available for inspection at https://github.com/dbrademan/IPSA-dev for custom implementations. This repository contains the raw data, sequence databases, and peptide identifications utilized in the manuscript.
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