Enhancing a Mass Spectrometry I/O Framework

Managing the I/O and organization of mass spectrometry data in the form of files and structures within a program is often time consuming due to the many fields that need to be set and retrieved. Each programmer handling this in his/her own way leads to incompatibilities and inefficiencies between implementations. The Mass Spectrometry I/O Project addresses these issues by creating a framework that handles mass spectrometry data I/O and data organization thereby allowing researchers to concentrate on data analysis rather than I/O. In addition, the Mass Spectrometry I/O Project leverages several cross platform and portability enhancing technologies, allowing it to be utilized on a wide variety of hardware and operating system combinations. Mass spectrometers are used in proteomics to determine the mass/charge ratio and abundance of the various peptide fragments that comprise a particular peptide or protein (5). The basic operation of a mass spectrometer involves placing a sample in the inlet, ionizing the sample, separating the ionized sample using methods such as electromagnetic fields, and detecting the separated particles. There are various types of mass spectrometers that use different ionization types such as matrix-assisted laser desorption/ionization (MALDI), and electrospray ionization (ESI), each of which takes a different approach to ionizing and separating the particles that comprise a sample. Each type of mass spectrometer is best suited for particular tasks as each method of ionization and detection has its own advantages and disadvantages. There is problem of incompatible data formats, and a lack of infrastructure to handle mass spectrometry data due to the use of proprietary file formats. With the ever increasing number of mass spectrometry data file formats, it becomes difficult and time consuming for programmers to handle these I/O and data management challenges (3). The Mass Spectrum I/O Project (MSIOP) was designed to address these problems, allowing for the use of data from a multitude of mass spectrometers, while providing a sound infrastructure that includes input, output, and data type conversion, upon which mass spectrometry tools can be built (5).