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 the conversion of raw data files into 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 are 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.

在生物学领域，特别是在蛋白质和肽科学领域，质谱仪的强大之处在于它适用于广泛的应用领域。质谱可用于鉴定复杂混合物中的蛋白质和肽，鉴定和定位翻译后修饰，将蛋白质和肽的结构表征到最详细的水平，或检测蛋白质-配体的非共价相互作用。由于自由和开源软件（FOSS）的运动，科学家们拥有无限的机会来加深他们在软件开发方面的技能，以编写解决质谱数据分析问题的软件。将原始数据文件转换为开放标准格式文件后，现在可以在FOSS平台（例如GNU / Linux，并且仅适用于FOSS解决方案。这篇综述介绍了质谱分析打开文件格式的简要历史，并介绍了在蛋白质和肽段质谱研究领域中常用的FOSS项目：鉴定项目主要涉及自动化流程，例如蛋白质组学和肽组学以及生物技术。结构表征项目，通常涉及对质量数据的手动检查。最后一种项目通常涉及软件，该软件允许用户以面向图形的交互式方式深入研究海量数据。因此，根据以下标准对软件项目进行了分类：面向软件开发人员的软件库与基于桌面的图形用户界面，