Proximity proteomics data.

Proteomics data from biotin-enriched samples harvested as outlined in Fig 1F. Description of columns: Protein FDR Confidence: The confidence that the software has that the given protein is present in the sample. In most cases, we filter the data to show only high confident proteins. Accession: Uniprot or NCBI accession number. Description: Name of the protein, along with the species and gene name. The gene name can be found after “GN =“. Marked As: This column is present if multiple species were searched. It will show which database the given protein originated from. MW [kDa]: Molecular weight of the protein. # of Unique Peptides: Peptides can be shared between different proteins or protein isoforms, so this column shows the number of peptides that are unique to the given protein group. # of Peptides: The total number of unique and shared peptides for the given protein group. # of PSMs (Peptide Spectral Matches): Peptide spectral matches are MS2 scans that are matched to a peptide by the search algorithm. This differs from the number of peptides because the same peptide can be fragmented and identified multiple times within a mass spec run, especially if the protein that the peptide originated from was in high abundance. The number of PSMs will therefore always be greater than or equal to the number of peptides identified. Abundance Ratio (log2): The protein fold change in log2 format between the given samples or groups. The software caps the maximum fold change at 100, so the largest log2 fold change you will see is 6.64 (2^6.64 = 100). Abundance Counts: The number of peptides that are used to calculate the abundance of the given protein. Abundances (or Normalized Abundances): The sum of the peak areas for each peptide that could be integrated for the given protein. If normalization was selected, then the normalized abundances will be shown. (XLSX)