Table I.

List of 44 proteins annotated as tumor-derived proteins in xenograft-bearing mice

Identified peptides were divided into a group of human specific peptides (identified only in the IPI human database) and a group of homologous peptides (present in both the IPI human and IPI mouse database). Homologous peptides were annotated as tumor-derived when 4 or more times higher abundant in the serum of PC339 or PC346 xenografted-mice in comparison with control serum. Annotations are derived from the Gene Ontology database.

Protein name	Gene symbol	IPI accession no.	Human/homologue	No. of unique peptides	Sequence coverage	Xenograft	Molecular function	Biological process	Location
					%
14-3-3 protein γa	YWHAG	IPI00230707	Homologue	5	20.65	PC339	Protein kinase C binding	Regulation of signal transduction	Cytoplasm
14-3-3 protein θa	YWHAQ	IPI00018146	Human	4	15.92	PC339	Protein kinase C inhibitor activity	Regulation of progression through cell cycle	Cytoplasm
α-Enolasea	ENO1	IPI00465248	Human	4	26.67	PC339	Phosphopyruvate hydratase activity	Glycolysis	Cytoplasm
Apolipoprotein A-I precursor	APOA1	IPI00021841	Human	3	16.24	PC339	Lipid binding	Cholesterol metabolism	Secreted
Cathepsin Z precursor	CTSZ	IPI00002745	Homologue	2	5.61	PC346	Cysteine-type peptidase activity	Proteolysis	Lysosome
Chromosome 20 orf 114	C20orf114	IPI00291410	Human	2	4.34	PC346	Lipid binding
Coactosin-like protein	COTL1	IPI00017704	Homologue	2	9.15	PC339	Actin binding
Coagulation factor V	F5	IPI00406603	Homologue	6	3.55	PC339	Oxidoreductase activity	Blood coagulation	Secreted
Cofilin, non-muscle isoforma	CFL1	IPI00012011	Homologue	3	21.69	PC339	Protein binding	Cytoskeleton organization and biogenesis	Cytoplasm
Complement component C8 β chain precursor	C8B	IPI00294395	Homologue	2	5.66	PC339		Immune response	Secreted
Cytochrome c	CYCS	IPI00465315	Homologue	2	17.14	PC346/339	Heme binding	Caspase activation via cytochrome c	Mitochondrion matrix
Fructose-bisphosphate aldolase Aa	ALDOA	IPI00465439	Human/homologue	11	30.77	PC346/339	Fructose-bisphosphate aldolase activity	Glycolysis
Glutathione peroxidase 3 precursor	GPX3	IPI00026199	Human	5	23.01	PC339	Glutathione peroxidase activity	Hydrogen peroxide catabolism	Secreted
Glyceraldehyde-3-phosphate dehydrogenasea	GAPDH	IPI00219018	Human	7	25.97	PC346/339	Glyceraldehyde-3-phosphate dehydrogenase activity		Cytoplasm
Inter-α (globulin) inhibitor H3	ITIH3	IPI00028413	Homologue	2	3.03	PC346	Serine-type endopeptidase inhibitor activity	Hyaluronan metabolism	Secreted
Junction plakoglobin	JUP	IPI00554711	Homologue	2	2.81	PC339	Cytoskeletal protein binding	Cell adhesion
Lactate dehydrogenase Aa	LDHA	IPI00217966	Human/homologue	9	21.69	PC346/339	l-Lactate dehydrogenase activity	Anaerobic glycolysis	Cytoplasm
Lactate dehydrogenase Ba	LDHB	IPI00219217	Human	10	29.94	PC346/339	l-Lactate dehydrogenase activity	Anaerobic glycolysis	Cytoplasm
Lumican precursor	LUM	IPI00020986	Homologue	2	5.92	PC339	Collagen binding	Collagen fibril organization	Secreted
Lysozyme C precursor	LYZ	IPI00019038	Human/homologue	4	23.65	PC346/339	Lysozyme activity	Inflammatory response
Maltase-glucoamylase, intestinala	MGAM	IPI00220143	Human	3	1.18	PC346/339	Protein binding	Carbohydrate metabolism	Cell membrane
Myosin heavy chain, skeletal muscle, adult 2	MYH2	IPI00007856	Homologue	3	4.94	PC346	Actin binding
Myosin, light polypeptide 6, alkali, smooth muscle and non-muscle isoform 1	MYL6B	IPI00335168 IPI00413922	Homologue	3	14.42	PC339	Structural component of muscle	Muscle filament sliding
Nucleoside-diphosphate kinase A	NME1	IPI00012048	Human/homologue	6	46.71	PC339	Nucleoside-diphosphate kinase activity	Negative regulation of cell proliferation	Cytoplasm
Nucleoside-diphosphate kinase B	NME2	IPI00026260	Homologue	6	42.76	PC339	Nucleoside-diphosphate kinase activity	Negative regulation of cell proliferation	Cytoplasm
					%
Peroxiredoxin-2a	PRDX2	IPI00000874 IPI00027350	Human/homologue	3	13.13	PC339	Thioredoxin peroxidase activity	Antiapoptosis	Cytoplasm
Proteasome subunit α type 1	PSMA1	IPI00472442	Human/homologue	6	24.91	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit α type 2	PSMA2	IPI00219622	Homologue	5	22.64	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit α type 4	PSMA4	IPI00299155	Human	5	17.30	PC339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit α type 6	PSMA6	IPI00029623	Homologue	9	37.80	PC346	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit α type 7	PSMA7	IPI00024175	Human	6	21.37	PC339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 1	PSMB1	IPI00025019	Human/homologue	7	34.02	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 2	PSMB2	IPI00028006	Homologue	2	12.44	PC346	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 3a	PSMB3	IPI00028004	Homologue	3	18.05	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 4	PSMB4	IPI00556607	Human/homologue	5	17.80	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 5	PSMB5	IPI00479306	Human/homologue	10	38.78	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 6	PSMB6	IPI00000811	Human	3	12.97	PC346/339	Peptidase activity	Proteolysis	Cytoplasm
Proteasome subunit β type 8	PSMB8	IPI00000783	Homologue	2	5.88	PC346	Protein binding	Proteolysis	Cytoplasm
Prothrombin precursor	F2	IPI00019568	Homologue	2	2.25	PC346	Thrombin activity	Regulation of progression through cell cycle	Secreted
Splice isoform 1 of complement factor B precursor	CFP	IPI00639937	Homologue	2	4.90	PC346/339	Complement binding	Complement activation	Secreted
Thrombospondin-1 precursora	THBS1	IPI00296099	Homologue	7	7.26	PC346/339	Signal transducer activity	Cell motility	Secreted
Transcobalamin-2	TCN2	IPI00136556	Homologue	3	6.09	PC339	Cobalamin transporter activity	Cobalamin transport	Secreted
Triose-phosphate isomerase 1 varianta	TPI1	IPI00465028	Human/homologue	5	22.09	PC346/339	Triose-phosphate isomerase activity	Glycolysis
Voltage-dependent anion channel 2	VDAC2	IPI00455531	Homologue	2	7.77	PC346	Voltage-gated anion channel porin activity	Anion transport	Mitochondrion outer membrane

^aProteins that have earlier been identified by others in isolated exosomes from various origin.