FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2277691344> ?p ?o ?g. }

• W2277691344 abstract "This thesis describes the Ph.D. research project in Bioengineering for Computational Proteomics carried out during the last three years (January 2008 - January 2011). Activities focused on design and development of methods for the analysis of Quantitative Mass Spectrometry-based Proteomics data. The Introduction briefly elucidates the main themes developed in the thesis and how the work was schemed. It reviews the computational issues associated to both data handling and quantification, and introduces the solutions proposed in the following.The first two chapters are introductory to the Proteomics and Mass Spectrometry field. The objective is to provide the reader with the information needed to understand Quantitative Mass Spectrometry-based Proteomics. In particular, Chapter 1 explains how proteomics was born, as the –omics science of proteins. Then proteomics main applications and goals are illustrated, which are ranging from clinics and pharmaceutics to systems biology. Chapter 2 shows the main technologies and instrumentation exploited in Mass Spectrometry-based proteomics. The most common experimental setups are reported: among them, the Liquid Chromatography-Mass Spectrometry (LC-MS) technique is thoroughly explained since it is the principal technique for Quantitative Mass Spectrometry-based Proteomics.The third Chapter presents the main concepts necessary to introduce the reader to the main topic of the PhD research Project, that is the development of bioinformatics tools for the handling and quantification of Mass Spectrometry-based Quantitative Proteomics data, focusing on LC-MS quantitative data and their analysis. Indeed, LC-MS data are highly informative for quantification aims, but challenging to parse. Data features that were pivotal for the design of the proposed solutions (i.e., the 3D structure of LC-MS data and the high quality profile acquisition) are highlighted. In the fourth Chapter, the state of art both for data handling and quantification is described and available standard data formats and software are illustrated as well as related open challenges.In Chapter 5, the dataset used to carry out the analyses is technically described. It consists of LC-MS data from a labeled controlled mixture of proteins with known quantification ratios, acquired in profile acquisition mode and in triplicates.In particular, this thesis presents 2 software solutions to address the handling and quantification of Quantitative Mass Spectrometry-based Proteomics data: mzRTree and 3DSpectra, respectively. Chapter 6 presents the solution proposed for the data handling issue. The proposal is a scalable 2D indexing approach implemented through an R-tree-based data structure, called mzRTree, that relies on a sparse matrix representation of the dataset, which is appropriate for LC-MS data, and more in generally for MS-based proteomics data. mzRTree allows efficient data access, storage and enables a computationally sustainable analysis of profile MS data.Regarding the quantification, which is one of the most relevant problem in mass spectrometry-based proteomics, Chapter 7 illustrates the solution proposed for the quantification problem: 3DSpectra. It is an innovative quantification algorithm for LC-MS labeled profile data exploiting both the 3-dimensionality of data and the profile acquisition. 3DSpectra fits on peptide data the 3D isotopic distribution model shaped by a Gaussian Mixture Model including a noise component, using the Expectation-Maximization approach. This model enables the software to both recognize the borders of the 3D isotopic distribution and reject noise. 3DSpectra is a reliable and accurate quantification strategy for labeled LC-MS data, providing significantly wide and reproducible proteome coverage.In the conclusion section of this thesis future and ongoing research work, regarding further development of both the mzRTree data structure and 3DSpectra quantification software, are discussed." @default.
• W2277691344 created "2016-06-24" @default.
• W2277691344 creator A5041642048 @default.
• W2277691344 date "2011-01-30" @default.
• W2277691344 modified "2023-09-27" @default.
• W2277691344 title "MASS SPECTROMETRY-BASED PROTEOMICS: A 3D APPROACH TO DATA HANDLING AND QUANTIFICATION" @default.
• W2277691344 cites W1967370206 @default.
• W2277691344 cites W1971983473 @default.
• W2277691344 cites W1980297970 @default.
• W2277691344 cites W1982468602 @default.
• W2277691344 cites W1996701734 @default.
• W2277691344 cites W1997504014 @default.
• W2277691344 cites W2004411627 @default.
• W2277691344 cites W2023096047 @default.
• W2277691344 cites W2023655541 @default.
• W2277691344 cites W2025574846 @default.
• W2277691344 cites W2027603999 @default.
• W2277691344 cites W2034541601 @default.
• W2277691344 cites W2038249420 @default.
• W2277691344 cites W2046441184 @default.
• W2277691344 cites W2047356598 @default.
• W2277691344 cites W2052388444 @default.
• W2277691344 cites W2057761395 @default.
• W2277691344 cites W2061575335 @default.
• W2277691344 cites W2068016108 @default.
• W2277691344 cites W2068241704 @default.
• W2277691344 cites W2072671787 @default.
• W2277691344 cites W2073292063 @default.
• W2277691344 cites W2089686959 @default.
• W2277691344 cites W2099192586 @default.
• W2277691344 cites W2103107953 @default.
• W2277691344 cites W2104764521 @default.
• W2277691344 cites W2107231094 @default.
• W2277691344 cites W2107710616 @default.
• W2277691344 cites W2109606373 @default.
• W2277691344 cites W2110174460 @default.
• W2277691344 cites W2110211303 @default.
• W2277691344 cites W2111208057 @default.
• W2277691344 cites W2118269922 @default.
• W2277691344 cites W2120907797 @default.
• W2277691344 cites W2124260943 @default.
• W2277691344 cites W2133111499 @default.
• W2277691344 cites W2135995285 @default.
• W2277691344 cites W2145361425 @default.
• W2277691344 cites W2147443546 @default.
• W2277691344 cites W2403542553 @default.
• W2277691344 cites W2460368520 @default.
• W2277691344 cites W2496665356 @default.
• W2277691344 cites W2793216206 @default.
• W2277691344 cites W3002576394 @default.
• W2277691344 cites W3102442597 @default.
• W2277691344 cites W1498445097 @default.
• W2277691344 hasPublicationYear "2011" @default.
• W2277691344 type Work @default.
• W2277691344 sameAs 2277691344 @default.
• W2277691344 citedByCount "0" @default.
• W2277691344 crossrefType "journal-article" @default.
• W2277691344 hasAuthorship W2277691344A5041642048 @default.
• W2277691344 hasConcept C104317684 @default.
• W2277691344 hasConcept C162356407 @default.
• W2277691344 hasConcept C185592680 @default.
• W2277691344 hasConcept C2522767166 @default.
• W2277691344 hasConcept C41008148 @default.
• W2277691344 hasConcept C43617362 @default.
• W2277691344 hasConcept C46111723 @default.
• W2277691344 hasConcept C55493867 @default.
• W2277691344 hasConcept C80311884 @default.
• W2277691344 hasConceptScore W2277691344C104317684 @default.
• W2277691344 hasConceptScore W2277691344C162356407 @default.
• W2277691344 hasConceptScore W2277691344C185592680 @default.
• W2277691344 hasConceptScore W2277691344C2522767166 @default.
• W2277691344 hasConceptScore W2277691344C41008148 @default.
• W2277691344 hasConceptScore W2277691344C43617362 @default.
• W2277691344 hasConceptScore W2277691344C46111723 @default.
• W2277691344 hasConceptScore W2277691344C55493867 @default.
• W2277691344 hasConceptScore W2277691344C80311884 @default.
• W2277691344 hasLocation W22776913441 @default.
• W2277691344 hasOpenAccess W2277691344 @default.
• W2277691344 hasPrimaryLocation W22776913441 @default.
• W2277691344 hasRelatedWork W14197325 @default.
• W2277691344 hasRelatedWork W2008400428 @default.
• W2277691344 hasRelatedWork W2011061591 @default.
• W2277691344 hasRelatedWork W2015888228 @default.
• W2277691344 hasRelatedWork W2038498399 @default.
• W2277691344 hasRelatedWork W2040069681 @default.
• W2277691344 hasRelatedWork W2109691687 @default.
• W2277691344 hasRelatedWork W2126527016 @default.
• W2277691344 hasRelatedWork W2169579508 @default.
• W2277691344 hasRelatedWork W2223110466 @default.
• W2277691344 hasRelatedWork W2335879448 @default.
• W2277691344 hasRelatedWork W2340055481 @default.
• W2277691344 hasRelatedWork W2389645433 @default.
• W2277691344 hasRelatedWork W2430002620 @default.
• W2277691344 hasRelatedWork W2511502622 @default.
• W2277691344 hasRelatedWork W2551129957 @default.
• W2277691344 hasRelatedWork W2582573331 @default.
• W2277691344 hasRelatedWork W2802654440 @default.
• W2277691344 hasRelatedWork W2886265233 @default.
• W2277691344 hasRelatedWork W3011000061 @default.
• W2277691344 isParatext "false" @default.

• next