Mass Spectrometry Data Format Standards in Proteomics

Mass spectrometry (MS) is currently the most commonly used technology for the identification of proteins. In MS data processing, multiple strategies are frequently used to analyze MS data, and the data analysis pipeline is always divided into multiple subtasks with support of multiple software tools in each subtask. One problem of MS data processing is the non-uniform data format, which may affect MS data exchange and integration. It may lead to some challenges in the development of MS data processing platform (MSDPP) and the construction of MS databases. Studying on MS data format standards can not only provide a way to summarize information needed in MS data processing methods, but also be beneficial to the development of MSDPP. In this manuscript, some MS data format standards developed in recent years are introduced. Then, the advantage and disadvantage of each standard are summarized as well as its application, and some possible improvements of MS data format standards are proposed.