Analysis of MS Results
This protocol is extracted from research article:
Identification of the Bok Interactome Using Proximity Labeling
Front Cell Dev Biol, May 31, 2021; DOI: 10.3389/fcell.2021.689951

The MS data for each TurboID fusion protein underwent two stages of refinement (depicted in Supplementary Figure 3). In the first stage, for each experiment (i) proteins were excluded from further analysis if the q value > 0.01, (ii) keratin proteins were excluded, and (iii) proteins were included only if they were unique or if abundance was 5× increased in TurboID samples versus control samples (abundance = peptide spectrum match number divided by the total number of amino acids in the parent protein). In the second stage, lists of included proteins from a number (n) of independent experiments were compared, and proteins were considered to be “strongly labeled” if they were present in multiple (e.g., at least 6/7) lists. For each TurboID construct, lists of proteins after the first stage of refinement, plus the strongly labeled proteins, are shown in Supplementary Tables 14. Protein localization is described in the Supplementary Methods.

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