Abstract
We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement.
Highlights
With recent technological advances in liquid chromatography–mass spectrometry (LC-MS) instrumentation, quantitation strategies and computational methods for MS data analysis, it has become possible to identify and quantify thousands of proteins in a single shotgun proteomics experiment [1,2,3]
We developed a descriptive web server, the Proteomics Identifications and Quantitations Data Management and Integration Service (PIQMIe) that aids in reliable management, analysis and visualization of semi-quantitative MSbased proteomics experiments
The analysis focused on the protein composition and changes in the extracellular compartments, namely the extracellular matrix (ECM) and matrix vesicles (MVs) (Supplementary Table S1)
Summary
With recent technological advances in liquid chromatography–mass spectrometry (LC-MS) instrumentation, quantitation strategies and computational methods for MS data analysis, it has become possible to identify (to infer) and quantify thousands of proteins in a single shotgun proteomics experiment [1,2,3]. Further analyses of processed MS data, namely of those on peptide and protein (group) identifications and quantitations, are often facilitated by stand-alone, platform-specific spreadsheet tools including Microsoft Excel or dedicated Perseus software (http://www.perseus-framework.org). These tools are useful, they are not suitable for data management and integration, nor are scalable with increasing amounts of input data as compared to a database management or an information retrieval system [7]. The above issues motivated us to seek a light-weight, cross-platform and open-source solution that equips a proteomics researcher with a dedicated tool for data management, integration and analysis of peptide and protein lists obtained from the MaxQuant software. The web server provides data access through a web interface and supports programmatic access through the RESTful JSONbased web service [17]
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