Several factors should be considered when choosing proteomics software. Tools to assess post-acquisition QC, including inspection of the chromatograms and spectras, to examine the raw signal to troubleshoot issues and tune settings, and tools to compare injections across time to assess LCMS performance, are useful. Additionally, tools to perform post-acquisition analysis, such as peptide/protein identification and quantification, and tools to gain biological insights are also important. However, for both post-acquisition QC and analysis, proteomics data analysis software should be scalable, easy-to-use, and high-performing, and should enable automation and support data storage/management.