Fig. 1: Master AMT DB of the mitochondrial proteome.

a The overall scheme of AMT DB construction. A total of 80 datasets (18 × 3 + 24) were generated from LC-MS/MS analysis. Each dataset was processed by iPE-MMR, after which a target-decoy MS-GF+ search was performed (peptide identification). The resultant peptides (or identified UMCs) were used to construct the AMT DB. b, c Utilization of the AMT DB to assign peptide IDs to unidentified UMCs. The 42,132 AMTs (magenta dots) in the AMT DB are visualized in a 2D (NET and molecular weight) scatter plot (left). For a LC-MS/MS dataset, the identified UMCs (blue dots) are shown in the upper right scatter plot. By matching the unidentified UMCs in this dataset with AMTs using the indicated mass and NET tolerances, a subset of unidentified UMCs was assigned to peptide IDs of matching AMTs. These matched UMCs (red dots) are shown in the bottom right scatter plot