Plant Proteomic Data Acquisition and Data Analyses: Lessons from Spaceflight

Proteomics has the capacity to identify and quantify the proteins present in a sample. The technique has been used extensively across all model organisms to study various physiological processes and signaling pathways. In addition to providing a global view of regulatory processes inside a cell, proteomics can also be used to identify candidate genes and retrieve information on alternative isoforms of known proteins. Here, we provide protocols for protein extraction from Arabidopsis thaliana seedlings and describe analysis techniques used after data collection. This approach was originally used for the Biological Research in Canisters (BRIC) 20 spaceflight experiment but is valid for any ground-based or flight experiment. Extraction protocols for soluble and membrane proteins and basic analysis and quality metrics for MS/MS data are provided. Avenues for data analysis post-MS/MS data acquisition and details of software that can be used in gathering structural data on proteins of interest are also included. Use of differential abundance and network-based approaches for proteomics data analyses can reveal regulatory patterns not apparent through differential abundance or transcriptomic data alone.