Table 3 Mass spectrometry results from MASCOT and LFQ Maxquant analysis

Mascot Data	IP:FLAG on transiently transfected cells
	IP:FLAG on FLAGSLY cells				IP:FLAG on empty-pcDNA3.1 cells
	Score	Nber peptides	% Sqce covery	EmPAI	Score	Nber peptides	% Sqce covery	EmPAI
HDAC3	86	1	3	0.1	0	0	0	0
TBL1XR1	143	4	11	0.8	0	0	0	0
NCOR1	0	0	0	0	0	0	0	0
SLY	566	16	51	8.56	0	0	0	0
TBL1X	273	7	0.8	24	0	0	0	0

MaxQuant Data	IP:FLAG on whole testis		IP:FLAG on transiently transfected cells
	IP:FLAG on FLAGSLY testis	IP:FLAG on WT testis	IP:FLAG on FLAGSLY cells	IP:FLAG on empty- pcDNA3.1 cells
	LFQ	LFQ	LFQ	LFQ
HDAC3	0	0	141 110	0
TBL1XR1	0	0	45 558	0
NCOR1	92 305	0	0	0
SLY	6 544 900	0	5 026 100	0
TBL1X	0	0	754 720	0

Abbreviations: EmPAI, Exponentially Modified Protein Abundance Index; LFQ, label-free quantification
Top panel: MASCOT analysis of the co-immunoprecipitation assay performed on whole testis and of the co-immunoprecipitation assay performed on GC1 cells. The protein score is the sum of the highest MS/MS ions score for each distinct peptide sequence. The highest the protein score, the more it is represented in the sample. However, for an identical mole of protein, a larger protein can give more peptides than a smaller one. EmPAI value provides a complementary information as it depends on the number of detected peptides compared to the total number of detectable peptides. The higher the EmPAI, the more abundant the protein.
Bottom panel: Maxquant LFQ analyses of the co-immunoprecipitation assay performed on whole testis and of the co-immunoprecipitation assay performed on GC1 cells. Maxquant analysis is more accurate than EmPAI because it reflects the total LC-MS intensity of peptides for the proteins

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