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Table 4 Lists of differentially expressed peptides in HCC and normal sample.

From: Enhanced peptide quantification using spectral count clustering and cluster abundance

HCC sample

Related

Cancer

Gene Name

Shogun Sequence

#(HCC) a

XCorr

Q Score

Protein Name

PMID c

HCC

AKR1B10

IVENIQVFDFK

2

2.04

0.95

Aldo-keto reductase family 1 member B10

20388846

 

ALB

DVFLGMFLYEYAR

2

2.04

0.96

Putative uncharacterized protein ALB

20658536

 

ECHDC3

VIIISAEGPVFSSGHDLK

2

2.14

0.95

Isoform 1 of Enoyl-CoA hydratase domain-containing protein 3, mitochondrial

21495032

 

EEF1A2

THINIVVIGHVDSGK

3

2.29

0.83

Elongation factor 1-alpha 2

18161050

 

EEF2

AYLPVNESFGFTADLR

3

3.30

0.96

Elongation factor 2

18161940

 

ENO1

FTASAGIQVVGDDLTVTNPK

33

2.51

0.61

Isoform alpha-enolase of Alpha-enolase

18813785

 

FGG

EGFGHLSPTGTTEFWLGNEK

2

3.16

0,95

Isoform Gamma-B of Fibrinogen gamma chain

19596924

 

FN1

SSPVVIDASTAIDAPSNLR

2

2.45

0.96

Isoform 1 of Fibronectin

16820872

 

FTCD

EAQELSLPVVGSQLVGLVPLK

2

2.98

0.99

Isoform A of Formimidoyltransferase-cyclodeaminase

18571811

 

GAPDH

WGDAGAEYVVESTGVFTTMEK

5

3.57

0.96

Glyceraldehyde-3-phosphate dehydrogenase

20714864

 

HBD

FFESFGDLSSPDAVMGNPK

2

2.37

0.96

Hemoglobin subunit delta

9214599

 

HMOX1

ALDLPSSGEGLAFFTFPNIASATK

2

2.82

0.90

Heme oxygenase 1

20664735

 

HRSP12

IEIEAVAIQGPLTTASL

2

2.31

0.98

Ribonuclease UK114

18349270

 

HSPA5

NQLTSNPENTVFDAK

4

2.51

0.97

HSPA5 protein

19445531

 

HSPA9

VINEPTAAALAYGLDK

2

2.04

0.93

Stress-70 protein, mitochondrial

18334731

  

DIVMTQSPDSLAVSLGER

2

2.52

0.99

  
 

HSPD1

ALMLQGVDLLADAVAVTMGPK

3

2.66

0.95

60 kDa heat shock protein, mitochondrial

21533669

 

NME1

VMLGETNPADSKPGTIR

2

2.57

0.97

Isoform 1 of Nucleoside diphosphate kinase A

17594820

  

EISLWFKPEELVDYK

2

2.27

0.95

  
 

P4HB

VDATEESDLAQQYGVR

2

2.38

0.81

Protein disulfide-isomerase

21207424

 

PRDX6

LIALSIDSVEDHLAWSK

3

3.48

0.93

Peroxiredoxin-6

19893992

 

TKT

ILATPPQEDAPSVDIANIR

3

2.16

0.98

cDNA FLJ54957, highly similar to Transketolase

17321041

 

VCP

LIVDEAINEDNSVVSLSQPK

2

2.49

0.98

Transitional endoplasmic reticulum ATPase

12560433

 

VIM

EMEENFAVEAANYQDTIGR

3

3.28

0.99

Vimentin

19843643

breast cancer

EEF1D

SLAGSSGPGASSGTSGDHGELVVR

2

3.17

0.93

Elongation factor 1-delta

17997862

 

HBB

GTFATLSELHCDK

2

2.09

0.97

Hemoglobin subunit beta

20097481

colon cancer

ACTN1

GYEEWLLNEIR

3

2.03

0.99

Alpha-actinin-1

17898132

  

ACLISLGYDVENDR

2

2.09

0.94

  
 

ATP5B

DQEGQDVLLFIDNIFR

2

2.58

0.98

ATP synthase subunit beta, mitochondrial

20080835

 

HMGCS2

LMFNDFLSASSDTQTSLYK

3

2.87

0.93

Hydroxymethylglutaryl-CoA synthase, mitochondrial

16940161

colorectral cancer

ATP5A1

NVQAEEMVEFSSGLK

2

2.65

0.95

ATP synthase subunit alpha, mitochondrial

9261598

  

EVAAFAQFGSDLDAATQQLLSR

3

2.88

0.87

  

Leukemia

IDH1

SIEDFAHSSFQMALSK

2

2.53

0.97

Isocitrate dehydrogenase [NADP] cytoplasmic

21205756

pancreatic cancer

EPPK1

LLEAQIATGGVIDPVHSHR

2

2.64

0.97

epiplakin 1

18498355

lung cancer

FGB

DNENVVNEYSSELEK

3

2.57

0.97

Fibrinogen beta chain

20142248

cell migration.

FLNB

YAPTEVGLHEMHIK

2

2.02

0.97

Isoform 1 of Filamin-B

20110358

 

XRCC5

YAPTEAQLNAVDALIDSMSLAK

5

3.60

0.94

ATP-dependent DNA helicase 2 subunit 2

 
 

AP1B1

LAPPLVTLLSAEPELQYVALR

2

2.81

0.99

Isoform A of AP-1 complex subunit beta-1

 
 

PLEC

AGTLSITEFADMLSGNAGGFR

2

2.16

0.89

Isoform 1 of Plectin-1

 
 

SDHAF2

PAPEIFENEVMALLR

3

2.41

0.93

Protein EMI5 homolog, mitochondrial

 
 

TUBA4A

AFVHWYVGEGMEEGEFSEAR

2

2.40

0.98

Tubulin alpha-4A chain

 
  

AVFVDLEPTVIDEVR

2

2.23

0.98

  
 

TYMP

DVTATVDSLPLITASILSK

3

2.84

0.93

Thymidine phosphorylase

 
 

UGP2

TLDGGLNVIQLETAVGAAIK

2

2.98

0.94

Isoform 1 of UTP--glucose-1-phosphate uridylyltransferase

 
 

TUBB

AILVDLEPGTMDSVR

2

1.97

0.95

Tubulin beta chain

 
 

TPI

VTNGAFTGEISPGMIK

2

2.52

0.95

Triosephosphate isomerase (Fragment)

 
 

Unknown

LFIGGLSFETTEESLR

2

2.64

0.97

Putative uncharacterized protein HNRNPA2B1

 
  

SVPTSTVFYPSDGVATEK

3

2.77

0.93

cDNA FLJ54957, highly similar to Transketolase

 
  

RHVFGESDELIGQK

2

2.09

0.96

  
  

VFSNGADLSGVTEEAPLK

2

2.24

0.90

PRO2275

 

Normal sample

Related Cancer

Gene Name

Shogun Sequence

#(normal)b

XCorr

Q Score

Protein Name

PMIDc

HCC

A2M

VSVQLEASPAFLAVPVEK

2

2.36

0.93

Alpha-2-macroglobulin

18959789

  

LLLQQVSLPELPGEYSMK

3

2.25

0.96

  
 

ACTA2

YPIEHGIITNWDDMEK

3

2.42

0.96

Actin, aortic smooth muscle

21214675

 

ALB

RPCFSALEVDETYVPK

2

2.18

0.90

Putative uncharacterized protein ALB

20658536

 

ALDH2

VAEQTPLTALYVANLIK

2

2.55

0.86

Aldehyde dehydrogenase, mitochondrial

20186752

 

ALDH6A1

ENTLNQLVGAAFGAAGQR

2

2.46

0.89

Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial

17786358

  

LFIHESIHDEVVNR

2

2.61

0.96

  
  

VNAGDQPGADLGPLITPQAK

2

3.27

0.98

  
 

ALDOB

GILAADESVGTMGNR

3

2.40

0.85

Fructose-bisphosphate aldolase B

17786358

  

ELSEIAQSIVANGK

2

2.32

0.96

  
 

ASL

INVLPLGSGAIAGNPLGVDR

3

3.18

0.76

Argininosuccinate lyase

19138817

 

ASS1

NPWSMDENLMHISYEAGILENPK

2

2.74

0.96

Argininosuccinate synthase

20104527

 

BHMT

ISGQEVNEAACDIAR

2

2.23

0.62

Betaine--homocysteine S-methyltransferase 1

19960509

  

AGPWTPEAAVEHPEAVR

2

2.62

0.93

  
 

C5orf33

VATQAVEDVLNIAK

2

2.23

0.97

Isoform 2 of UPF0465 protein C5orf33

21495032

 

CAT

GAGAFGYFEVTHDITK

2

2.17

0.78

Catalase

21324921

  

FNTANDDNVTQVR

2

2.40

0.92

  
 

FGG

AIQLTYNPDESSKPNMIDAATLK

3

3.76

0.92

Fibrinogen gamma chain

17018627

 

ETFA

LEVAPISDIIAIK

5

2.73

0.89

Electron transfer flavoprotein alpha-subunit

20515076

 

CPS1

TVLMNPNIASVQTNEVGLK

3

2.42

0.99

Isoform 1 of Carbamoyl-phosphate synthase [ammonia], mitochondrial

12143053

  

FLGVAEQLHNEGFK

3

2.67

0.97

  
  

AVNTLNEALEFAK

2

2.58

0.96

  
  

VLGTSVESIMATEDR

3

2.22

0.88

  
  

IEFEGQPVDFVDPNK

2

2.52

0.98

  
  

GLNSESMTEETLK

2

2.63

0.95

  
 

CYP3A7

EMVPIIAQYGDVLVR

2

2.37

0.80

Cytochrome P450 variant 3A7

17978482

 

DCI

DADVQNFVSFISK

3

2.20

0.99

Isoform 1 of 3,2-trans-enoyl-CoA isomerase, mitochondrial

1903293

 

ECHS1

ALNALCDGLIDELNQALK

2

3.33

0.98

Enoyl-CoA hydratase, mitochondrial

15492826

 

EIF5

AMGPLVLTEVLFNEK

5

2.41

0.83

Eukaryotic translation initiation factor 5

19175833

 

FBP1

LDVLSNDLVMNMLK

7

2.34

0.72

Fructose-1,6-bisphosphatase 1

19637194

 

FH

SGLGELILPENEPGSSIMPGK

3

2.20

0.98

Isoform Mitochondrial of Fumarate hydratase, mitochondrial

1958270

  

AAAEVNQDYGLDPK

3

2.23

0.97

  
  

IYELAAGGTAVGTGLNTR

2

2.24

0.97

  
 

FLNA

ASGPGLNTTGVPASLPVEFTIDAK

3

2.68

0.97

Isoform 2 of Filamin-A

21471709

 

HPD

SQIQEYVDYNGGAGVQHIALK

2

2.99

0.98

4-hydroxyphenylpyruvate dioxygenase

8558370

 

HSPA5

SQIFSTASDNQPTVTIK

2

2.16

0.97

HSPA5 protein

19445531

 

KRT8

LKLEAELGNMQGLVEDFK

59

2.08

0.43

Keratin, type II cytoskeletal 8

18932288

 

PBLD

VNTENLLQVENTGK

2

2.33

0.94

Phenazine biosynthesis-like domain-containing protein

20525558

 

PDIA4

EVSQPDWTPPPEVTLVLTK

3

2.49

0.98

Protein disulfide-isomerase A4

19016532

 

PEBP1

GNDISSGTVLSDYVGSGPPK

6

3.51

0.96

Phosphatidylethanolamine-binding protein 1

20739083

 

PHB

NITYLPAGQSVLLQLPQ

3

2.56

0.86

Prohibitin

21318481

 

PRDX6

ELAILLGMLDPAEK

4

2.00

0.94

Peroxiredoxin-6

19893992

 

SELENBP1

NTGTEAPDYLATVDVDPK

2

2.06

0.96

cDNA FLJ55757, highly similar to Selenium-binding protein 1

21338716

 

SORBS1

LTPVQVLEYGEAIAK

2

2.64

1.00

Isoform 9 of Sorbin and SH3 domain-containing protein 1

11374898

 

SORD

LENYPIPEPGPNEVLLR

2

1.99

0.97

Sorbitol dehydrogenase

12848999

 

STIP1

ALSVGNIDDALQCYSEAIK

2

2.54

0.97

Stress-induced-phosphoprotein 1

17627933

 

TPI1

VAHALAEGLGVIACIGEK

2

3.35

0.99

Isoform 2 of Triosephosphate isomerase

18813785

 

TXNDC5

ALAPTWEQLALGLEHSETVK

3

4.01

0.98

Thioredoxin domain-containing protein 5

16574106

 

Vκ3

EIVLTQSPATLSLSPGER

2

2.97

0.97

Rheumatoid factor D5 light chain (Fragment)

15207089

 

ADH1A

FSLDALITHVLPFEK

6

2.60

0.92

Alcohol dehydrogenase 1A

16054971

  

ELGATECINPQDYK

2

2.15

0.94

  
 

ADH4

ISEAFDLMNQGK

4

2.95

0.94

Isoform 2 of Alcohol dehydrogenase 4

16054971

  

GGVDFALDCAGGSETMK

3

3.25

0.96

  
  

FNLDALVTHTLPFDK

8

2.76

0.95

  
  

AAIAWEAGKPLCIEEVEVAPPK

3

2.71

0.99

  
  

DLHKPIQEVIIELTK

5

3.08

0.99

  

prostate cancer

COL6A2

YGGLHFSDQVEVFSPPGSDR

2

2.33

0.86

Isoform 2C2A' of Collagen alpha-2(VI) chain

18353764

  

LLTPITTLTSEQIQK

3

2.57

0.93

  
  

VAVVTYNNEVTTEIR

5

2.38

0.67

  
  

IEDGVPQHLVLVLGGK

2

2.01

0.86

  
 

RPS27A

TITLEVEPSDTIENVK

2

2.23

0.98

ubiquitin and ribosomal protein S27a precursor

15647830

breast cancer

EMILIN1

LVGSGLHTVEAAGEAR

2

2.47

0.96

EMILIN-1

16243817

 

MYH9

NLPIYSEEIVEMYK

2

2.06

0.97

Isoform 1 of Myosin-9

18796164

  

QLLQANPILEAFGNAK

3

2.80

0.86

Isoform 1 of Myosin-9

 
  

IAEFTTNLTEEEEK

13

2.29

0.65

Isoform 1 of Myosin-9

 

colon cancer

ALDH1A1

GYFVQPTVFSNVTDEMR

3

3.18

0.97

Retinal dehydrogenase 1

21435460

 

ATP5B

TVLIMELINNVAK

5

3.18

0.88

ATP synthase subunit beta, mitochondrial

20080835

 

ETFA

AAVDAGFVPNDMQVGQTGK

2

2.13

0.98

Electron transfer flavoprotein subunit alpha, mitochondrial

16708797

  

GTSFDAAATSGGSASSEK

6

2.53

0.86

  
 

ANXA6

GLGTDEDTIIDIITHR

2

2.48

0.98

annexin VI isoform 2

21137014

Leukemia

GLUD1

HGGTIPIVPTAEFQDR

2

2.48

0.98

Glutamate dehydrogenase 1, mitochondrial

19683518

 

IDH2

LNEHFLNTTDFLDTIK

3

2.77

0.98

Isocitrate dehydrogenase [NADP], mitochondrial

21205756

gastic carcinoma

HIST4H4

TVTAMDVVYALK

2

2.03

0.96

Histone H4

19139817

colorectal cancer

RRBP1

TLQEQLENGPNTQLAR

2

2.74

0.88

Isoform 3 of Ribosome-binding protein 1

19425502

pancreatic cancer

ARG1

TGLLSGLDIMEVNPSLGK

4

2.71

0.91

Isoform 1 of Arginase-1

21347333

 

CALM1

VFDKDGNGYISAAELR

3

2.50

0.93

Calmodulin

18852131

  

EAFSLFDKDGDGTITTK

2

2.62

0.98

  

ovarian cancer

HAAO

TQGSVALSVTQDPACK

2

2.56

0.91

Isoform 1 of 3-hydroxyanthranilate 3,4-dioxygenase

19724865

Lung cancer

ACY1

TVQPKPDYGAAVAFFEETAR

2

2.50

0.99

cDNA FLJ60317, highly similar to Aminoacylase-1

8394326

cell migration.

FLNB

LVSPGSANETSSILVESVTR

2

3.21

0.99

Isoform 1 of Filamin-B

19915675

 

UGP2

ILTTASSHEFEHTK

2

3.30

0.93

Isoform 1 of UTP--glucose-1-phosphate uridylyltransferase

 
  

IQRPPEDSIQPYEK

4

2.38

0.95

  
 

ALDH4A1

EEIFGPVLSVYVYPDDKYK

3

3.34

0,95

Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial

 
 

COL14A1

HFLENLVTAFDVGSEK

3

2.39

0.77

Isoform 1 of Collagen alpha-1(XIV) chain

 
 

DCTN2

LLGPDAAINLTDPDGALAK

2

2.24

0.94

dynactin 2

 
 

EEF1B2

SPAGLQVLNDYLADK

3

2.86

0.84

Elongation factor 1-beta

 
 

GRHPR

IAAAGLDVTSPEPLPTNHPLLTLK

3

3.11

0.99

Glyoxylate reductase/hydroxypyruvate reductase

 
 

HSD17B10

VMTIAPGLFGTPLLTSLPEK

3

2.80

0.91

Isoform 1 of 3-hydroxyacyl-CoA dehydrogenase type-2

 

PCBD1

VHITLSTHECAGLSER

2

2.54

0.96

Pterin-4-alpha-carbinolamine dehydratase

 
 

PDIA6

GSTAPVGGGAFPTIVER

3

2.05

0.87

Isoform 2 of Protein disulfide-isomerase A6

 
 

PTGR1

HFVGYPTNSDFELK

2

2.24

0.93

Prostaglandin reductase 1

 
  

TGPLPPGPPPEIVIYQELR

7

2.56

0.96

  
 

TF

SAGWNIPIGLLYCDLPEPR

3

2.65

0.97

Serotransferrin

 
  

EDPQTFYYAVAVVK

4

2.49

0.92

  
 

unknown

PAHVVVGDVLQAADVDK

2

2.88

0.96

22 kDa protein

 

HCC and normal sample

Related Cancer

Gene Name

Shogun Sequence

#(HCC)a /#(normal)b

XCorr

Q Score

Protein Name

PMIDc

HCC

CPS1

MEYDGILIAGGPGNPALAEPLIQNVR

2/11

3.92

0.91

carbamoyl-phosphate synthetase 1

12143053

  

SIFSAVLDELK

1/8

3.87

0.92

  
  

IAPSFAVESIEDALK

3/13

2.96

0.85

  
  

TAVDSGIPLLTNFQVTK

1/10

2.50

0.45

  
 

HBA1

VADALTNAVAHVDDMPNALSALSDLHAHK

1/8

3.67

0.93

Hemoglobin subunit alpha 1

20572306

  

VGAHAGEYGAEALER

4/13

2.05

0.94

  
 

P4HB

ILFIFIDSDHTDNQR

10/15

2.88

0.49

Protein disulfide-isomerase

21207424

 

HNRNPC

MIAGQVLDINLAAEPK

21/9

2.31

0.46

Heterogeneous nuclear ribonucleoprotein C (C1/C2), isoform CRA_b

20572306

 

PGK1

VSHVSTGGGASLELLEGK

16/8

3.36

0.46

Phosphoglycerate kinase 1

19200351

 

ACTB

DLYANTVLSGGTTMYPGIADR

10/3

3.25

0.96

Actin, cytoplasmic 1

16493704

 

GSTA1

NDGYLMFQQVPMVEIDGMK

2/6

2.24

0.83

Glutathione S-transferase

20604928

 

FABP1

SVTELNGDIITNTMTLGDIVFK

17/6

3.43

0.78

Fatty acid-binding protein

12245374

 

CES1

EGYLQIGANTQAAQK

13/1

2.21

0.76

Isoform 1 of Liver carboxylesterase 1

19658107

Breast Cancer

LGALS7/LGALS7B

LVEVGGDVQLDSVR

19/1

2.35

0.65

Galectin-7/p53-induced gene 1 protein

20382700

 

HBB

FFESFGDLSTPDAVMGNPK

39/67

2.72

0.74

Hemoglobin subunit beta

20097481

 

MDH2

VDFPQDQLTALTGR

4/7

2.49

0.93

Malate dehydrogenase 2

19485423

 

MYH9

LQQELDDLLVDLDHQR

9/15

2.54

0.56

Myosin, heavy polypeptide 9, non-muscle, isoform CRA_a

18796164

Ovarian cancer

PSMA2

YNEDLELEDAIHTAILTLK

3/5

4.48

0.84

Proteasome subunit alpha type-2

14960231

Lung cancer

AKR1A1

DPDEPVLLEEPVVLALAEK

3/5

3.16

0.63

Aldo-keto reductase family 1

17114299

Chromophobe renal cell carcinomas

ATP5H

NLIPFDQMTIEDLNEAFPETK

3/5

2.48

0.95

ATP synthase subunit d, mitochondrial

20440404

Leukemia

IGKC

VDNALQSGNSQESVTEQDSK

3/6

3.95

0.92

Ig kappa chain C region

12357370

 

RPS7

TLTAVHDAILEDLVFPSEIVGK

5/3

3.92

0.92

40S ribosomal protein S7

 
  1. a the number of spectral sets in HCC samples
  2. b the number of spectral set in normal samples.
  3. c the PubMed index for MEDLINE
  4. Table 4 shows lists of DEPs in HCC sample, normal sample, and both samples. In HCC sample and normal sample, 57 and 115 reference spectra were identified by SEQUEST. Among these spectra, 29 and 59 peptides were known biomarkers for the human liver cancer. In both sample, we performed a beta-binomial test for finding out DEPs. The result shows that only 84 out of 1,571 reference spectra indicate heterogeneity of spectral counts between HCC and normal tissue samples. Among these 84 reference spectra, only 22 were identified by SEQUEST.