Table 2.

Affinity purification-mass spectrometry experimental parameters reported in Dickinson et al. and Olson et al. ^&

	Dickinson et al.*	Olson et al.&
Tissue type	HeLa 229 cells	HeLa 229 cells
Inc-APEX2 construct	IncB-APEX2	IncF-APEX2, IncA-APEX2, IncATM-APEX2
Affinity Purification	Streptavidin-agarose resin	Streptavidin Magnetic beads
Elution	On resin trypsin digestion	SDS-PAGE and sectioned
Digestion Enzyme(s)	Trypsin	Trypsin and AspN
Mass Spectrometer	Thermo Fisher Velos Orbitrap	Thermo Fisher Orbitrap Lumos
Software	MS-GF+ Release (v2016.10.24)	Mascot and Scaffold
Protein modifications	Carbamidomethyl and Oxidation	Carbamidomethyl and Oxidation
Fasta search Homo sapiens	UniProt SPROT accessed 20170412	UniProt Human accessed 20180927
Fasta search C. trachomatis	C. trachomatis L2 434/Bu pL2 Plasmid accessed 20180105	C. trachomatis L2 434/Bu accessed 20180330
Peptide/protein Filtering	False Discovery Rate ≤ 1%, Unique peptides, requiring a minimum of six amino acids in length, were filtered using an MS-GF threshold of ≤ 1×10−9, corresponding to an estimated false-discovery rate (FDR) <1% at a peptide level.	Scaffold filtering: 95% protein threshold, 1-peptide minimum, 95% peptide threshold
Additional data processing	Relative peptide abundances were log-transformed. Elimination of statistical outliers was confirmed using a standard Pearson correlation at a sample level
Statistical Test	G-test and T-test	SAINT#

^*previously published in Dickinson et al., PLoS Pathog. 2019 15(4):e1007698, doi: 10.1371/journal.ppat.1007698

^&previously published in Olson et al., Infection and Immunity. 2019

^#Significance Analysis of INTeractome (SAINT)