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A data integration framework and a software suite for mass spectrometry-based Proteomics
LC-MS/MS based proteomics evolved quickly in the past few years. It is now very common to produce thousands of MS spectra per hour leading to identification of thousands of peptides and proteins. However, computational tools didn’t evolve as fast as these technologies. The main issue is not related to the availability of tools but rather to their performance and their user-friendliness. Most recent software allow running these pipelines from a single interface, simplifying thus the tasks of users but they still suffer from a number of drawbacks dependency on a given instrumentation, lack of a graphical user interface (GUI) offering an overview of the pipeline results, and more importantly they do not enable global analysis based on the different fractionation levels of a same experimental design.
Efficently extract, store, analyse and explore proteomics results
The aim of the ProFI WP2 is to develop “Proline”, a computational platform which can perform a set of proteomics data computations and present the obtained results through user-friendly GUIs. Proline algorithms focus on: result validation (using custom filters and target decoy analysis), merge/comparison of datasets, label-free quantification (spectral count and LC-MS analyses). Mascot and OMSSA results are currently supported because of the nature of the Proline data persistence layer, which is based on a relational database extended with flexible JSON annotations. Other search engines will further be supported. Using an efficient, structured and extensible persistence layer allows Proline to handle large-scale proteomic studies issued from many different analytical strategies. Proline “core” is composed of a set of tasks based on modules that users can execute on a remote server through Proline GUIs. This execution strategy efficiently shifts the heavy computation workload from the user’s local hardware to shared dedicated resources.
Finally, two independent GUIs are available for data browsing. Proline Studio GUI, has a tight integration with the user desktop environment and provides highly interactive components. Proline Web GUI, allows accessing the data remotely from a web browser and binds output results with online resources.