In the field of biology, and specifically in protein and peptide science, the power of mass spectrometry is that it is applicable to a vast spectrum of applications. Mass spectrometry can be applied to identify proteins and peptides in complex mixtures, to identify and locate post-translational modifications, to characterize the structure of proteins and peptides to the most detailed level or to detect protein-ligand non covalent interactions. Thanks to the Free and Open Source Software (FOSS) movement, scientists have limitless opportunities to deepen their skills in software development to code software that solves mass spectrometric data analysis problems. After conversion of raw data files to open standard format files, the entire spectrum of data analysis tasks can now be performed integrally on FOSS platforms, like GNU/Linux, and only with FOSS solutions. This review presents a brief history of mass spectrometry open file formats and goes on with the description of FOSS projects that are commonly used in protein and peptide mass spectrometry fields of endeavor: identification projects that involve mostly automated pipelines, like proteomics and peptidomics, and bio-structural characterization projects that most often involve manual scrutiny of the mass data. Projects of the last kind usually involve software that allows the user to delve into the mass data in an interactive graphics-oriented manner. Software projects were thus categorized on the basis of these criteria: software libraries for software developers vs desktop-based graphical user interface software for the end user and automated pipeline-based data processing vs interactive graphics-based mass data scrutiny.