multiplierz: an extensible API based desktop environment for proteomics data analysis

We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines.Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Mass spectrometry-based proteomics, particularly liquid chromatography coupled to electrospray ionization, has become the predominant technique for identification and quantification of proteins in biological systems [1]. Growing demand for improved annotation of primary proteomics data with biological information from various public databases has catalyzed interest in the development of software tools to support integration of these data types. Unfortunately, a number of factors, including lack of experimental standardization, rapid introduction of novel mass spectrometry technology, and the evolution of proprietary file formats associated with proteomics platforms represent a significant hurdle to the development of efficient and comprehensive software frameworks.To accommodate the emergent nature of proteomics-related technologies and the burgeoning number of databases that contain various biological annotations, data analytic systems must emphasize (i) intuitive and inter