CHAPTER 18: MASSyPup64: Linux Live System for Mass Spectrometry Data Processing

The installation of software, especially open source, can be cumbersome because of the differences in the target operating systems. Thus, installation issues are a major obstacle for the distribution of novel programs. Possible workarounds for this situation include (1) the development of web-services (e.g., XCMS Online; see Chapter 8), (2) defined programming/installation environments on top of a host operating system (e.g. Docker; see Chapter 19) and (3) integrated systems that bundle the operating system and the programs (e.g., MASSyPup64, discussed in this chapter). MASSyPup64 integrates multiple mass spectrometry (MS) and helper programs on a Linux live system, and provides all the necessary functions, programming languages, and libraries. Moreover, the system does not require installation on a hard drive and can be used directly from a USB boot medium. The latest release of MASSyPup64, additionally, provides Docker and webserver capabilities. This chapter introduces the concept of MASSyPup64 and explains how it differs from Docker. It also explains the steps involved in the preparation and booting of a live USB drive. As a practical example, the determination of the molecular weight of a protein from electrospray ionisation mass spectrometry data using MASSyPup64 is demonstrated. In addition, the modification of the live system to create their own versions of MASSyPup64 is shown. This ‘remastering’ process allows the users to easily prepare custom flavours of MASSyPup64, for instance, to distribute data and new programs or to build a uniform informatics environment for courses.