Table I.

Samples used for peptidome analysis and identified peptide number

Patient diagnosis n = 8		Gender	Sample and passage n = 28	ID	Samples weight (mg)	Total peptides identified (5% FDR)		After reverse, contaminant, length & mouse filtering		Peptide number fold change PDX vs human biopsy
						In specific sample	In specific patient	In specific sample	In specific patient
Head and neck	Adnexal adenocarcinoma	M	Human biopsy	P1-human biopsy-1	<13*	392	734	212	488	10
			Human biopsy	P1-human biopsy-2	<13*	442		359
			PDX p3	P1-PDX-1	260	4804	5864	4196	4949
			PDX p3	P1-PDX-2	290	4713		4124
			PDX p3	P1-PDX-3	135	3089		2745
Bile duct	Cholangiocarcinoma	M	Human biopsy	P2-human biopsy	60	157		17		18
			PDX p0	P2-PDX-p0–1	355	417	536	218	309
			PDX p0	P2-PDX-p0–2	258
			PDX p3	P2-PDX-p3–1	287	473		280
			PDX p3	P2-PDX-p3–2	337
Lung	N/A	M	Human biopsy	P3-human biopsy	120	549		258		2
			PDX p0	P3-PDX	250	775		416
Gastric	Carcinoma	M	Human biopsy	P4-human biopsy	100	1095		515		1
			PDX p1	P4-PDX	200	872		556
Vascular	Hemangioendothelioma	F	Human biopsy	P5-human biopsy	<13*	804		643		0.1
			PDX p0	P5-PDX	100	244		80
Head and neck	Squamous cell carcinoma	M	Human biopsy	P6-human biopsy	<13*	1146		1018		2
			PDX p0	P6-PDX-p0–1	100	1907	2660	1498	2095
			PDX p0	P6-PDX-p0–2	1121
			PDX p0	P6-PDX-p0–3	1163
			PDX p3	P6-PDX-p3–1	1086	2068		1671
			PDX p3	P6-PDX-p3–2	1289
Bladder	Sarcomatoid carcinoma	M	Human biopsy	P7-human biopsy	<13*	437		344		2
			PDX p0	P7-PDX	120	784		715
Pancreatic	Adenocarcinoma	F	Human biopsy	P8-human biopsy-1	50	131	1241	86	985	2
			Human biopsy	P8-human biopsy-2	1177	1182		951
			PDX p1	P8-PDX-p1	1079	1387	2635	1129	2122
			PDX p2	P8-PDX-p2	120	1988		1765
			PDX p3	P8-PDX-p3	1142	1503		1189

^*Needle biopsy-exact weight unknown. Indicated weight is for a 14G needle which results in <13 mg cores.