Table II. Representative selection of proteins identified from immunoprecipitates.

Where multiple isoforms or subunits of the same protein were identified, just one isoform or subunit is listed here so that an impression of the spectrum of proteins identified can be obtained. The full comparison of proteins identified is presented in supplementalTable S4.

Protein name	Accession number	Number of patient precipitates containing protein (total = 3)	Number of control precipitates containing protein (total = 3)	Number of paired patient and control precipitates both containing protein (total = 3)
Membrane proteins identified
MuSK; muscle, skeletal, receptor tyrosine kinase	IPI00289243	3	0	0
Intracellular proteins found in both patient and control immunoprecipitates
ACTB; actin, cytoplasmic 1	IPI00021439	1	1	0
DDX1; ATP-dependent RNA helicase DDX1	IPI00293655	2	1	1
FUS; isoform short of RNA-binding protein FUS	IPI00221354	2	1	0
HNRNPA1; isoform A1-B of heterogeneous nuclear ribonucleoprotein A1	IPI00215965	3	3	3
HNRNPA2B1; isoform B1 of heterogeneous nuclear ribonucleoproteins A2/B1	IPI00396378	3	3	3
HSPA9; stress-70 protein, mitochondrial precursor	IPI00007765	3	2	2
IGHG4; IGHG4 protein	IPI00550640	3	1	1
ILF2; interleukin enhancer-binding factor 2	IPI00005198	2	2	1
TUBB; tubulin β chain	IPI00011654	1	1	1
Intracellular proteins found in either patient or control immunoprecipitates
ACTB; actin, cytoplasmic 2	IPI00848058	0	1	0
DDX17; DEAD box polypeptide 17 isoform 1	IPI00023785	0	1	0
HNRPH1; heterogeneous nuclear ribonucleoprotein H	IPI00013881	0	1	0
IGHG1; IGHG1 protein	IPI00829944	0	1	0
ILF3; isoform 1 of interleukin enhancer-binding factor 3	IPI00298788	0	1	0
PRDX4; peroxiredoxin-4	IPI00011937	0	1	0
RPL35; 60 S ribosomal protein L35	IPI00412607	1	0	0
TUBB2C; tubulin β-2C chain	IPI00007752	1	0	0
VIM; vimentin	IPI00418471	0	1	0