title: MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing.
abstract: One of the major bottlenecks in the proteomics field today resides in the computational interpretation of the massive data generated by the latest generation of high-throughput MS instruments. MS/MS datasets are constantly increasing in size and complexity and it becomes challenging to comprehensively process such huge datasets and afterwards deduce most relevant biological information. The Mass Spectrometry Data Analysis (MSDA, https://msda.unistra.fr) online software suite provides a series of modules for in-depth MS/MS data analysis. It includes a custom databases generation toolbox, modules for filtering and extracting high-quality spectra, for running high-performance database and de novo searches, and for extracting modified peptides spectra and functional annotations. Additionally, MSDA enables running the most computationally intensive steps, namely database and de novo searches, on a computer grid thus providing a net time gain of up to 99% for data processing.
authors.affiliation: Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Carapito
authors.forename: Alexandre
authors.initials: A
authors.lastname: Burel
authors.forename: Patrick
authors.initials: P
authors.lastname: Guterl
authors.forename: Alexandre
authors.initials: A
authors.lastname: Walter
authors.forename: Fabrice
authors.initials: F
authors.lastname: Varrier
authors.forename: Fabrice
authors.initials: F
authors.lastname: Bertile
authors.forename: Alain
authors.initials: A
authors.lastname: Van Dorsselaer
mesh_terms: D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins
keywords: Bioinformatics; Computational proteomics; Database searching; De novo sequencing; Functional annotations; Grid computing