Quantitative Proteome Analysis of Colorectal-Cancer-Related Differential Proteins

Online Resource 1

“Quantitative proteome analysis of colorectal-cancer-related differential proteins”

Yanbin Zhang1 · Yue Liu1 · Yingjiang Ye2 · Danhua Shen2 · Hui Zhang2 · Hongyan Huang1 · Sha Li1 · Shan Wang2 · Jun Ren1

Journal of Cancer Research and Clinical Oncology

Corresponding author:

Jun Ren, MD, PhD.

Beijing Key Lab for Therapeutic Cancer Vaccines, Capital Medical University Cancer Center, Beijing Shijitan Hospital, the Capital Medical University, Beijing, China.

Tel: +86-10-63926300, Fax: +86-10-63926298, E-mail:

Table S1 Clinicopathological characteristics of 20 CRC patients for LCM

PT# / Sex / Age / Location / Diameter
(cm) / T
stage / N
stage / M
stage / Overall
stage / Grade
1 / Female / 78 / Descending colon / 2 / 3 / 0 / 0 / IIA / Moderate
2 / Female / 66 / Sigmoid colon / 6 / 4 / 0 / 0 / IIB / Poor
3 / Male / 69 / Rectum / 3.5 / 3 / 0 / 0 / IIA / Poor
4 / Male / 66 / Rectum / 4 / 3 / 0 / 0 / IIA / Moderate
5 / Male / 82 / Rectum / 7 / 3 / 0 / 0 / IIA / Moderate
6 / Female / 58 / Rectum / 3.5 / 3 / 0 / 0 / IIA / Poor
7 / Male / 61 / Rectum / 4.5 / 3 / 1 / 0 / IIA / Poor
8 / Male / 75 / Ascending colon / 2.5 / 3 / 0 / 0 / IIA / Moderate
9 / Male / 50 / Rectum / 3 / 3 / 0 / 0 / IIA / Moderate
10 / Male / 45 / Rectum / 4.5 / 3 / 0 / 0 / IIA / Moderate
11 / Male / 83 / Ascending colon / 3 / 3 / 0 / 0 / IIA / Moderate
12 / Male / 74 / Rectum / 2.7 / 2 / 0 / 0 / I / Moderate
13 / Female / 72 / Rectum / 4 / 3 / 1 / 0 / IIIB / Moderate
14 / Male / 96 / Sigmoid colon / 2.5 / 3 / 0 / 0 / IIA / Moderate
15 / Female / 64 / Rectum / 4 / 3 / 0 / 0 / IIA / Moderate
16 / Female / 74 / Ascending colon / 3 / 3 / 0 / 0 / IIA / Moderate
17 / Female / 55 / Rectum / 5 / 3 / 0 / 0 / IIA / Moderate
18 / Female / 59 / Rectum / 5.2 / 3 / 0 / 0 / IIA / Moderate
19 / Female / 53 / Sigmoid colon / 7.5 / 4 / 1 / 0 / IIIB / Poor
20 / Female / 73 / Ascending colon / 3 / 3 / 0 / 0 / IIA / Moderate

Table S2Significantly differential proteins identified

IPI number / Protein name / Ratio
(cancer/normal) / Cellular component (GO) / Biological process (GO) / Functional network (IPA)
IPI00293276.9 / Macrophage migration inhibitory factor / 9.95 / extracellular space / signal transduction, cell proliferation, cell death
IPI00399234.3 / Cyclic nucleotide gated channel alpha / 6.91 / protein complex / ion transport / cell morphology
IPI00304925.3 / Heat shock 70 kDa protein 1 / 4.89 / endoplasmic reticulum, mitochondrion / nucleotide and nucleic acid metabolism, cell death
IPI00218200.7 / B-cell receptor-associated protein 31 / 4.72 / endoplasmic reticulum, Golgi apparatus, plasma membrane / protein transport, cell death / cell growth and proliferation
IPI00018465.1 / T-complex protein 1 subunit eta / 4.57 / amino acid metabolism
IPI00216308.4 / Voltage-dependent anion-selective channel protein 1 / 4.55 / mitochondrion, plasma membrane / ion transport, cell death / cellular assembly and organization
IPI00023004.6 / Eukaryotic translation initiation factor 1A, Y-chromosomal / 4.39 / carbohydrate metabolism
IPI00220642.6 / 14-3-3 protein gamma / 4.35 / cytoplasm / signal transduction, cell differentiation, protein transport / cell growth and proliferation
IPI00555692.2 / ANXA4 protein / 4.19 / inflammatory response
IPI00010896.2 / Chloride intracellular channel protein 1 / 4.12 / cytosol, plasma membrane / signal transduction, ion transport / carbohydrate metabolism
IPI00550363.2 / Transgelin-2 / 4.05 / carbohydrate metabolism
IPI00604620.3 / Nucleolin / 3.85 / nucleolus / binding / cellular assembly and organization
IPI00026167.2 / NHP2-like protein 1 / 3.75 / nucleolus / nucleotide and nucleic acid metabolism, cell organization and biogenesis / carbohydrate metabolism
IPI00216318.5 / 14-3-3 protein beta / 3.71 / cytosol, microtubule organizing center, cytoskeleton / signal transduction, protein transport, cell death / cell growth and proliferation
IPI00220362.4 / 10 kDa heat shock protein, mitochondrial (HSP10) / 3.70 / mitochondrion / cell death / cell growth and proliferation
IPI00007765.5 / Stress-70 protein, mitochondrial precursor (Mortalin) / 3.56 / mitochondrion / protein transport, cell death / cell growth and proliferation, amino acid metabolism, carbohydrate metabolism
IPI00027463.1 / Protein S100-A6 / 3.56 / nuclear membrane / signal transduction, cell proliferation, cell cycle / cell growth and proliferation
IPI00216319.3 / 14-3-3 protein eta / 3.55 / cytoplasm / signal transduction, cell differentiation, nucleotide and nucleic acid metabolism, protein transport / cell growth and proliferation
IPI00005198.2 / Interleukin enhancer-binding factor 2 / 3.37 / nucleolus / nucleotide and nucleic acid metabolism / inflammatory response
IPI00025512.2 / Heat-shock protein beta-1 / 3.21 / cytoskeleton / cell death / cell growth and proliferation
IPI00022649.3 / Isoform 1 of Solute carrier family 12 member 2 / 3.16 / plasma membrane / signal transduction, ion transport, cell homeostasis / cellular assembly and organization
IPI00397864.3 / Putative uncharacterized protein / 3.14
IPI00472102.3 / Heat shock protein 60 / 2.97 / cell growth and proliferation
IPI00410714.4 / Hemoglobin subunit alpha / 3.08 / cytosol / transport, binding
IPI00171087.7 / S1 RNA binding domain / 3.07
IPI00031804.1 / Isoform 1 of Voltage-dependent anion-selective channel protein 3 / 3.04 / mitochondrion / cell-cell signaling, ion transport / amino acid metabolism
IPI00016513.5 / Ras-related protein Rab-10 / 3.03 / Golgi apparatus, plasma membrane / signal transduction, protein transport / inflammatory response
IPI00006510.1 / Tubulin beta-1 chain / 3.00 / cytoskeleton / cell organization and biogenesis / cell morphology
IPI00184195.2 / 19 kDa protein / 3.12 / cell growth and proliferation
IPI00008433.4 / 40S ribosomal protein / 2.98 / cytosol / biosynthesis, translate / amino acid metabolism
IPI00029048.2 / Tubulin--tyrosine ligase-like protein / 2.94 / amino acid metabolism
IPI00013860.3 / 3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor / 2.78 / mitochondrion / nucleotide and nucleic acid metabolism, amino acid metabolism / amino acid metabolism
IPI00007188.4 / ADP/ATP translocase 2 / 2.76 / mitochondrion, plasma membrane / transport / cellular assembly and organization
IPI00018146.1 / 14-3-3 protein theta / 2.74 / microtubule organizing center, cytoskeleton / nucleotide and nucleic acid metabolism / cell growth and proliferation
IPI00002520.1 / Serine hydroxymethyltransferase, mitochondrial / 2.73 / mitochondrion / amino acid metabolism / inflammatory response
IPI00218448.4 / Histone H2A.Z / 2.68 / chromosome / nucleotide and nucleic acid metabolism, cell organization and biogenesis / inflammatory response
IPI00102165.3 / H2A histone family, member J isoform 1 / 2.68 / cellular assembly and organization
IPI00298363.2 / Far upstream element-binding protein 2 / 2.60
IPI00647012.2 / Heat shock 70kDa protein / 2.57
IPI00167368.2 / Isoform 1 of NMDA receptor-regulated 1-like protein / 2.52
IPI00465430.5 / 70 kDa protein / 2.52 / cell growth and proliferation
IPI00067659.1 / PREDICTED: similar to Nuclear transport factor / 2.50
IPI00009901.1 / Nuclear transport factor / 2.50 / nuclear membrane, cytosol / protein transport / embryonic development
IPI00788181.1 / PREDICTED: similar to Eukaryotic translation initiation factor 1A / 2.41
IPI00218097.3 / 145kDA protein / 2.40 / cell morphology
IPI00444262.1 / CDNA FLJ45706 fis, clone FEBRA2028457, highly similar to Nucleolin / 2.36
IPI00215884.4 / splicing factor, arginine/serine-rich 1 / 2.36 / nucleoplasm / nucleotide and nucleic acid metabolism / cell growth and proliferation
IPI00154668.5 / Coiled-coil domain-containing protein 93 / 2.35 / amino acid metabolism
IPI00013079.2 / EMILIN-1 / 2.34 / nucleolus, microtubule organizing center, cytoskeleton / cell adhesion / cell morphology
IPI00759644.1 / FK506 binding protein 12 / 2.33
IPI00735531.1 / PREDICTED: proline-rich synapse-associated protein 2 isoform / 2.32
IPI00513791.2 / Dedicator of cytokinesis 7 / 2.32 / cell differentiation, cell organization and biogenesis / cell growth and proliferation
IPI00009150.1 / Isoform 1 of suppressor of G2 allele of SKP1 homolog / 2.26 / cell growth and proliferation
IPI00010402.2 / Hypothetical protein / 2.20 / cell homeostasis / embryonic development
IPI00453473.5 / Histone H4 / 2.18 / nucleoplasm, chromosome / signal transduction, nucleotide and nucleic acid metabolism, cell organization and biogenesis
IPI00008575.3 / Isoform 1 of KH domain-containing, RNA-binding, signal transduction-assosciated protein / 2.17 / nucleus, membrane,organelle / signal transduction, cell proliferation, nucleotide and nucleic acid metabolism, cell cycle / cell growth and proliferation
IPI00021828.1 / Cystatin B / 2.16 / inflammatory response
IPI00014424.1 / Elongation factor 1-alpha 2 / 2.14 / nucleus, cytoplasm, organelle / cell death / carbohydrate metabolism
IPI00010720.1 / T-complex protein 1 subunit epsilon / 2.12 / nucleolus, cytosol / binding, macromolecule metabolism / amino acid metabolism
IPI00219005.2 / FK506-binding protein 4 / 2.12 / nucleolus / ion transport / cell growth and proliferation
IPI00305031.6 / B-lymphocyte antigen CD19 / 2.09 / plasma membrane / signal transduction / inflammatory response
IPI00455457.4 / Novel protein similar to histone 2, H3c / 2.09 / chromosome / nucleotide and nucleic acid metabolism, cell organization and biogenesis
IPI00255145.5 / PREDICTED: hypothetical protein / 2.08
IPI00298743.4 / Frizzled-5 / 2.06 / Golgi apparatus, plasma membrane / signal transduction, cell differentiation / embryonic development
IPI00414127.3 / Ran-specific GTPase-activating protein / 2.06 / microtubule organizing center, cytoskeleton / signal transduction, cell cycle, cell organization and biogenesis / cellular assembly and organization
IPI00171134.5 / Girdin / 2.05 / cytosol, endoplasmic reticulum, Golgi apparatus, plasma membrane / cell proliferation, nucleotide and nucleic acid metabolism, amino acid metabolism, cell organization and biogenesis / cellular assembly and organization
IPI00418497.1 / Isoform 2 of Import inner membrane translocase subunit TIM50, mitochondrial precursor / 2.01 / amino acid metabolism
IPI00216071.2 / Eosinophil lysophospholipase / 0.49 / cell morphology
IPI00217966.7 / Lactate dehydrogenase A / 0.49 / cytosol / binding, macromolecule metabolism / inflammatory response, cellular assembly and organization
IPI00018783.1 / Inosine triphosphate pyrophosphatase / 0.49 / cytoplasm / nucleotide and nucleic acid metabolism / cell morphology
IPI00016321.2 / Butyrophilin-like 8 short form / 0.49
IPI00442073.5 / Cysteine and glycine-rich protein / 0.48 / cell morphology
IPI00747752.1 / 25 kDa protein / 0.48
IPI00023598.2 / Tubulin beta-4 chain / 0.48 / cytoskeleton, plasma membrane, cilium / cell organization and biogenesis / cell growth and proliferation
IPI00072955.2 / Hypothetical protein KIAA1426 / 0.47 / carbohydrate metabolism
IPI00008934.1 / Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor / 0.46 / mitochondrion / biosynthesis / cell morphology
IPI00012493.1 / 40S ribosomal protein S20 / 0.46 / cytosol / biding, biosynthesis, macromolecule metabolism, translation / inflammatory response
IPI00395769.2 / Isoform Heart of ATP synthase gamma chain, mitochondrial precursor / 0.46 / amino acid metabolism
IPI00022228.2 / Vigilin / 0.45 / plasma membrane / binding, transport / inflammatory response, carbohydrate metabolism
IPI00012303.1 / Selenium-binding protein 1 / 0.45 / nucleus, cytoplasm, membrane, organelle / protein transport
IPI00553177.1 / Alpha-1-antitrypsin precursor / 0.45 / nucleolus / response to stimulus, binding / cellular assembly and organization
IPI00293853.3 / Cell surface A33 antigen precursor / 0.44 / plasma membrane / signal transducer activity / embryonic development
IPI00217185.1 / Isoform 2 of Ryanodine receptor / 0.44 / cell morphology
IPI00430820.1 / IGKV1-5 protein / 0.44 / carbohydrate metabolism
IPI00010099.1 / X-linked interleukin-1 receptor accessory protein-like 2 / 0.43 / membrane / signal transduction
IPI00015671.3 / Tubulin, alpha-like 3 / 0.43 / cytoskeleton / cell organization and biogenesis
IPI00007321.1 / Isoform 1 of Acyl-protein thioesterase 1 / 0.42 / amino acid metabolism
IPI00147874.1 / Sialic acid synthase / 0.39 / cytosol / biosynthesis, macromolecule metabolism / amino acid metabolism
IPI00215780.4 / 40S ribosomal protein S19 / 0.38 / nucleolus, cytosol / cell differentiation, nucleotide and nucleic acid metabolism, cell organization and biogenesis / embryonic development
IPI00016862.1 / Isoform Mitochondrial of Glutathione reductase, mitochondrial precursor / 0.39 / cytosol, mitochondrion / cell homeostasis / inflammatory response
IPI00031410.1 / FKBP12-rapamycin complex-associated protein / 0.39 / cytosol / signal transduction, cell organization and biogenesis / cell growth and proliferation
IPI00028888.1 / Isoform 1 of Heterogeneous nuclear ribonucleoprotein D0 / 0.39 / chromosome / nucleotide and nucleic acid metabolism / cell growth and proliferation, cellular assembly and organization
IPI00008438.1 / 40S ribosomal protein S10 / 0.38 / cytosol / binding, biosynthesis, macromolecule metabolism, translation / amino acid metabolism
IPI00796600.1 / 18 kDa protein / 0.38
IPI00792693.1 / Protein / 0.37 / cell growth and proliferation
IPI00215804.4 / PREDICTED: similar to Keratin, type II cytoskeletal / 0.37
IPI00217469.2 / Histone H1.1 / 0.37 / chromosome / nucleotide and nucleic acid metabolism, cell organization and biogenesis / carbohydrate metabolism
IPI00217467.2 / Histone H1.4 / 0.37 / chromosome / nucleotide and nucleic acid metabolism, cell organization and biogenesis / amino acid metabolism
IPI00022793.4 / Trifunctional enzyme beta subunit, mitochondrial precursor / 0.36 / mitochondrion / inflammatory response
IPI00060143.1 / Protein FAM3D / 0.36 / extracellular region / cell-cell signaling
IPI00009407.7 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 / 0.36 / endoplasmic reticulum / cell death / cellular assembly and organization
IPI00396174.4 / Coiled-coil domain-containing protein 25 / 0.36 / embryonic development
IPI00009822.1 / Signal recognition particle 54 kDa protein / 0.35 / nucleolus, nucleoplasm / protein transport / embryonic development
IPI00383046.3 / Carboxymethylenebutenolidase-like / 0.35 / carbohydrate metabolism
IPI00031045.3 / Destrin isoform b / 0.34
IPI00020986.2 / Lumican precursor / 0.33 / cellular assembly and organization
IPI00478114.2 / 16 kDa protein / 0.33
IPI00221093.6 / 40S ribosomal protein S17 / 0.33 / cytosol / nucleotide and nucleic acid metabolism, cell organization and biogenesis / carbohydrate metabolism
IPI00414603.3 / PREDICTED: similar to 40S ribosomal protein S17 isoform 1 / 0.33
IPI00473014.4 / Destrin / 0.33 / cytoskeleton / cell organization and biogenesis, / inflammatory response
IPI00478733.1 / 12 kDa protein / 0.31 / chromosome / nucleotide and nucleic acid metabolism, cell organization and biogenesis
IPI00009750.1 / Galectin-4 / 0.31 / cytosol, plasma membrane / cell adhesion / embryonic development
IPI00304962.3 / Collagen alpha-2(I) chain / 0.31 / plasma membrane / signal transduction / cellular assembly and organization
IPI00152584.1 / SLTP001 / 0.31 / amino acid metabolism
IPI00017926.1 / CDNA: FLJ22714 fis, clone / 0.31
IPI00382751.1 / Mast cell tryptase beta Ⅲ / 0.30 / embryonic development
IPI00009790.1 / 6-phosphofructokinase type C / 0.30 / cytosol / binding, macromolecule metabolism / cell growth and proliferation, carbohydrate metabolism
IPI00413826.2 / PREDICTED: similar to H3 histone / 0.30
IPI00141938.4 / H2A histone family, member V isoform 2 / 0.28 / chromosome / nucleotide and nucleic acid metabolism, cell organization and biogenesis
IPI00219037.5 / Histone H2A.X / 0.28 / nucleoplasm, chromosome / nucleotide and nucleic acid metabolism, cell cycle, cell organization and biogenesis / cell morphology
IPI00000848.4 / Isoform 1 of Transmembrane protease, serine 13 / 0.28 / inflammatory response
IPI00027201.1 / Mucin-2 precursor / 0.28 / cell growth and proliferation
IPI00152409.1 / Anterior gradient protein 3 homolog precursor / 0.27 / embryonic development
IPI00007427.2 / AGR2 / 0.27 / embryonic development
IPI00013809.1 / Maleylacetoacetate isomerase / 0.27 / cytosol, mitochondrion / amino acid metabolism / embryonic development
IPI00787105.1 / PREDICTED: similar to ribosomal protein S19 / 0.27
IPI00171438.2 / Thioredoxin domain-containing protein 5 / 0.23 / endoplasmic reticulum / cell death, cell homeostasis / embryonic development
IPI00020131.1 / Son of sevenless homolog 1 / 0.23 / cytosol, plasma membrane / signal transduction / cell growth and proliferation
IPI00019449.1 / Nonsecretory ribonuclease precursor / 0.20 / vacuole / nucleotide and nucleic acid metabolism
IPI00012912.1 / Carnitine O-palmitoyltransferase 2, mitochondrial / 0.19 / mitochondrion / transport / inflammatory response, embryonic development
IPI00215983.2 / Carbonic anhydrase 1 / 0.19 / Golgi apparatus / binding / carbohydrate metabolism
IPI00218414.4 / Carbonic anhydrase 2 / 0.18 / cell growth and proliferation
IPI00074957.1 / Egl nine homolog 2 / 0.17 / nucleus, cytoplasm, organelle / signal transduction, cell homeostasis, cell organization and biogenesis / embryonic development
IPI00423462.5 / Hypothetical protein DKFZp686K18196 / 0.15
IPI00166866.3 / IGHA1 protein / 0.15
IPI00216271.4 / Isoform A of Inositol polyphosphate 5-phosphatase / 0.15
IPI00015911.1 / Dihydrolipoyl dehydrogenase, mitochondrial precursor / 0.08 / mitochondrion, vacuole / cell differentiation, cell homeostasis / amino acid metabolism