Fig. 6

Comparison of the output from the three Protein-SIP approaches: SIPPER, MetaProSIP, and Calis-p. Four datasets were processed by expert operators for each approach using optimal parameters for each approach. The outputs from each tool were filtered for comparability by retaining only distinct protein unique peptides (PUPs), defined as peptides unique to a protein sequence and with a unique combination of sequence, charge state, and m/z. a Median.¹³C values were determined for organisms with 9 or more peptides. The expected ¹³C atom % value for each experimental condition was subtracted from each experimental SIP value and the deviation of the experimental value from the expected value is displayed. b Table showing the total number of protein unique peptides identified and used as the input for each approach and the total for which isotope values were quantified. c Summary of the parameters used for each tool/approach and additional post-processing steps as recommended by each expert operator. Each tool output was filtered for distinct protein unique peptides, i.e., isotope values were only used if the peptide could be uniquely assigned to a single species. MetaProSIP required an additional post-processing step for selecting the highest relative isotope abundance (RIA) value in cases where the tool reported multiple RIA values. Detailed data for this figure is shown in Figure S4 and Tables S7–S10