In line with genomics, proteomics has rapidly emerged as a promising field of research enabling the elucidation of numerous life sciences questions [1]. The tremendous progresses in mass spectrometry-based techniques over the last 20 years have led to the possibility to generate massive, highly accurate, qualitative and quantitative mass spectrometry data for very complex protein mixtures. The main bottleneck in proteomics research today resides in the interpretation of such massive data and new informatics/bioinformatics resources are strongly needed to support the emergence of the field [2]. The proteomists and computer scientists of the Hubert Curien Pluridisciplinary Institute (IPHC, Strasbourg, France) have interfaced open-source proteomics data interpretation tools on the EGI (European Grid Infrastructure) grid. Hence, by allowing higher throughput and larger scale proteomics projects to be solved, our MSDA pipeline (Mass Spectrometry Data Analysis, https://msda.unistra.fr/) offers important time gain factors. It also opens new fields of applications that were previously unreachable due to a lack of computing resources. The originalities of the use of the EGI grid infrastructure for this pipeline are described in this article.