Table 2. Relative quantification by label-free spectral counting of cetuximab-resistant protein expression.

			HT-29b			LIM1215b
Protein Acca	Gene Namea	Protein Descriptiona	Rsc (PBS v bevacizumab)	Rsc (PBS v cetuximab)	Rsc (PBS v Combination)	Rsc (PBS v bevacizumab)	Rsc (PBS v cetuximab)	Rsc (PBS v Combination)	Associated functiona
P68371	TUBB4B	Tubulin beta-4B chain	−2.2	−1.0	1.2	48.1	28.3	52.1	cytoskeleton remodelling, cytotoxicity
P07437	TUBB	Tubulin beta chain (Tubulin beta-5 chain)	−2.6	1.2	1.1	31.9	16.6	36.5	cytoskeleton remodelling, cytotoxicity
P00338	LDHA	L-lactate dehydrogenase A chain	2.7	2.8	5.0	21.1	12.2	26.7	Cellular metabolic process, glycolytic process
P61204	ARF3	ADP-ribosylation factor 3	15.0	1.1	10.6	8.0	11.9	4.9	Cellular metabolic process, glycolytic process
P06576	ATP5B	ATP synthase subunit beta, mitochondrial	−25.7	−1.7	−8.5	10.7	11.5	13.3	Cellular metabolic process, generation of precursor metabolites and energy
P62820	RAB1A	Ras-related protein Rab-1A	16.0	1.1	19.9	8.7	8.8	12.7	Signal transduction
P06733	ENO1	Alpha-enolase	−3.0	1.1	−2.3	20.7	7.9	22.8	Glycolytic process
P84085	ARF5	ADP-ribosylation factor 5	11.1	1.1	8.3	6.6	7.2	5.6	Signal transduction
P18085	ARF4	ADP-ribosylation factor 4	5.1	1.5	4.0	7.3	7.2	8.8	Signal transduction, apoptotic process
P31946	YWHAB	14-3-3 protein beta/alpha	34.9	1.1	33.8	30.1	5.6	29.2	Apoptotic process
P62258	YWHAE	14-3-3 protein epsilon	32.9	1.9	28.0	27.2	5.6	29.2	Apoptotic process
P27348	YWHAQ	14-3-3 protein theta	22.0	1.1	28.0	25.1	5.6	25.2	Apoptotic process
P50454	SERPINH1	Serpin H1	−9.9	−2.3	−8.5	18.7	5.6	9.5	regulation of proteolysis
Q9H0U4	RAB1B	Ras-related protein Rab-1B	16.0	1.1	16.4	8.0	5.6	11.1	Signal transduction
O00303	EIF3F	Eukaryotic translation initiation factor 3 subunit F	−4.1	−2.6	−3.5	6.6	5.6	8.8	regulation of translational initiation
P31947	SFN	14-3-3 protein sigma	8.2	−3.2	9.9	25.8	4.9	26.8	Apoptotic process
P31943	HNRNPH1	Heterogeneous nuclear ribonucleoprotein H	−1.3	−2.2	1.4	11.5	4.9	12.7	regulation of RNA splicing
O75390	CS	Citrate synthase, mitochondrial	−3.4	−1.2	1.4	8.7	4.9	8.0	cellular carbohydrate metabolic process
P61158	ACTR3	Actin-related protein 3	−5.4	−1.5	−4.6	7.3	4.9	7.2	cytoskeleton remodelling
P49327	FASN	Fatty acid synthase	−11.9	1.4	−10.2	−20.2	−18.4	−18.4	Cellular metabolic process, lipid metabolism
Q08211	DHX9	ATP-dependent RNA helicase A	−5.4	1.3	−4.6	−16.6	−15.1	−15.1	ATP catabolic process
P11940	PABPC1	Polyadenylate-binding protein 1	−6.0	−1.2	−5.2	−12.0	−10.9	−10.9	cellular protein metabolic process
P35241	RDX	Radixin	−14.5	1.0	−12.5	−11.1	−10.1	−10.1	cytoskeleton remodelling
P07384	CAPN1	Calpain-1 catalytic subunit	−4.7	1.4	−4.1	−8.4	−7.6	−7.6	regulation of cell proliferation
P39656	DDOST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit	1.2	1.1	3.7	−1.5	−6.8	−6.8	Cellular metabolic process, glycolytic process
Q99613	EIF3C	Eukaryotic translation initiation factor 3 subunit C	1.2	1.1	2.6	−7.5	−6.8	−6.8	cellular protein metabolic process
Q14152	EIF3A	Eukaryotic translation initiation factor 3 subunit A	−8.0	1.1	−6.9	−17.5	−6.1	−15.9	cellular protein metabolic process
E7EX73	EIF4G1	Eukaryotic translation initiation factor 4 gamma 1	−5.4	−1.1	−4.6	−6.6	−6.0	−6.0	cellular protein metabolic process
Q9NYU2	UGGT1	UDP-glucose:glycoprotein glucosyltransferase 1	−4.1	−1.1	−3.5	−5.7	−5.2	−5.1	Cellular metabolic process, glycolytic process
Q01813	PFKP	6-phosphofructokinase type C	−8.6	−1.2	−7.4	−5.7	−5.2	−5.1	Cellular metabolic process, glycolytic process

^aProtein description, Gene name, UniProt acc, and molecular function annotated from UniProt (http://www.uniprot.org/)

^bNormalised spectral count ratio (Rsc) between datasets