Many QC materials can be used as ground-truth for benchmarking both data acquisition and data analysis methods and parameters with respect to peptide and protein identification or quantification. For instance, a known spiked-in peptide or protein, or whole proteomes mixed in known ratios, can be used to specifically evaluate if the acquired and analyzed data reflects the true changes in relative abundance in the sample. Data from some QC standards are also available in ProteomeXchange (Table ). This data can be used to quality control and benchmark data analysis methods, determining whether an issue is due to the measurement or the data analysis. This can be especially useful since different peptide identification approaches affect protein quantification in quantitative proteomics experiments . For instance in metaproteomics, a large search space can drastically affect identification depth and biological conclusions . Using external datasets provides independent confidence of chosen data analysis workflows.