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Journal of Analytical Science and Technology

Table 1 List of differentially abundant ECM proteins between passage #15 and #40 HDFs

From: Shotgun proteomics of extracellular matrix in late senescent human dermal fibroblasts reveals a down-regulated fibronectin-centered network

IPI accession no.a

Gene symbolb

Protein name

mol%c

Fold changed

#40

#15

Increased ECM proteins in late senescent HDFs

     

IPI00914848

SERPINE2

Isoform 2 of Glia-derived nexin

0.24

 

#40

IPI00306543

GDF15

Growth/differentiation factor 15

0.20

 

#40

IPI00026941

PRSS23

Serine protease 23

0.16

 

#40

IPI00179185

CPZ

Isoform 2 of Carboxypeptidase Z

0.10

 

#40

IPI00022229

APOB

Apolipoprotein B-100

0.02

 

#40

IPI00554711

JUP

Junction plakoglobin

0.08

 

#40

IPI00013933

DSP

Isoform DPI of Desmoplakin

0.03

 

#40

IPI00003176

HTRA1

Serine protease HTRA1

1.15

0.25

4.565

IPI00022937

F5

252 kDa protein

0.07

0.03

2.213

IPI00025753

DSG1

Desmoglein-1

0.15

0.08

1.881

IPI00022420

RBP4

Retinol-binding protein 4

0.52

0.28

1.814

IPI00027547

DCD

Dermcidin

2.04

1.16

1.762

IPI00218247

TIMP3

Metalloproteinase inhibitor 3

0.70

0.43

1.610

IPI00218918

ANXA1

Annexin A1

0.39

0.25

1.556

IPI00300725

KRT6A

Keratin, type II cytoskeletal 6A

1.70

1.15

1.478

Decreased ECM proteins in late senescent HDFs

     

IPI00873923

TGFBI

Transforming growth factor, beta-induced, 68 kDa, isoform CRA_a

 

9.98

#15

IPI00009890

SERPINE2

Isoform 1 of Glia-derived nexin

 

0.50

#15

IPI00218732

PON1

Serum paraoxonase/arylesterase 1

 

0.34

#15

IPI00221224

ANPEP

Aminopeptidase N

 

0.31

#15

IPI00029928

ELN

Elastin

 

0.24

#15

IPI00789324

JUP

cDNA FLJ60424, highly similar to Junction plakoglobin

 

0.21

#15

IPI00219682

STOM

Erythrocyte band 7 integral membrane protein

 

0.20

#15

IPI00009456

NT5E

5 ~ -nucleotidase

 

0.15

#15

IPI00027482

SERPINA6

Corticosteroid-binding globulin

 

0.13

#15

IPI00328609

SERPINA4

Kallistatin

 

0.13

#15

IPI00550731

IGKC

Putative uncharacterized protein

 

0.12

#15

IPI00022895

A1BG

Alpha-1B-glycoprotein

 

0.11

#15

IPI00479116

CPN2

Carboxypeptidase N subunit 2

 

0.10

#15

IPI00022395

C9

Complement component C9

 

0.09

#15

IPI00018305

IGFBP3

Insulin-like growth factor-binding protein 3

 

0.09

#15

IPI00294395

C8B

Complement component C8 beta chain

 

0.09

#15

IPI00879709

C6

Complement component 6 precursor

 

0.06

#15

IPI00022371

HRG

Histidine-rich glycoprotein

 

0.05

#15

IPI00025864

BCHE

Cholinesterase precursor

 

0.04

#15

IPI00294004

PROS1

Vitamin K-dependent protein S

 

0.04

#15

IPI00339223

FN1

Isoform 3 of Fibronectin

 

0.03

#15

IPI00017640

SLIT3

Isoform 1 of Slit homolog 3 protein

 

0.03

#15

IPI00017601

CP

Ceruloplasmin

 

0.02

#15

IPI00217182

DSP

Isoform DPII of Desmoplakin

 

0.02

#15

IPI00031008

TNC

Isoform 1 of Tenascin

 

0.02

#15

IPI00022200

COL6A3

Isoform 1 of Collagen alpha-3(VI) chain

 

0.02

#15

IPI00022488

HPX

Hemopexin

0.13

0.69

− 5.241

IPI00555812

GC

Isoform 1 of Vitamin D-binding protein

0.06

0.24

− 4.002

IPI00292530

ITIH1

Inter-alpha-trypsin inhibitor heavy chain H1

0.10

0.38

− 3.943

IPI00026314

GSN

Isoform 1 of Gelsolin

0.12

0.47

− 3.808

IPI00007960

POSTN

Isoform 1 of Periostin

0.07

0.24

− 3.502

IPI00022431

AHSG

cDNA FLJ55606, highly similar to Alpha-2-HS-glycoprotein

0.15

0.47

− 3.136

IPI00022426

AMBP

Protein AMBP

0.09

0.25

− 2.892

IPI00011252

C8A

Complement component C8 alpha chain

0.05

0.14

− 2.711

IPI00021841

APOA1

Apolipoprotein A-I

0.37

0.99

− 2.690

IPI00029739

CFH

Isoform 1 of Complement factor H

0.04

0.11

− 2.530

IPI00550991

SERPINA3

cDNA FLJ35730 fis, clone TESTI2003131, highly similar to ALPHA-1-ANTICHYMOTRYPSIN

0.38

0.94

− 2.501

IPI00305461

ITIH2

Inter-alpha-trypsin inhibitor heavy chain H2

0.27

0.67

− 2.478

IPI00032291

C5

Complement C5

0.03

0.08

− 2.259

IPI00032179

SERPINC1

Antithrombin-III

0.36

0.77

− 2.160

IPI00021857

APOC3

Apolipoprotein C-III

0.32

0.69

− 2.125

IPI00071509

PKP1

Isoform 2 of Plakophilin-1

0.03

0.07

− 2.033

IPI00021842

APOE

Apolipoprotein E

0.09

0.17

− 1.988

IPI00219365

MSN

Moesin

0.04

0.09

− 1.988

IPI00291866

SERPING1

Plasma protease C1 inhibitor

0.12

0.24

− 1.936

IPI00292946

SERPINA7

Thyroxine-binding globulin

0.07

0.13

− 1.920

IPI00478003

A2M

Alpha-2-macroglobulin

0.10

0.20

− 1.883

IPI00163207

PGLYRP2

Isoform 1 of N-acetylmuramoyl-L-alanine amidase

0.05

0.09

− 1.807

IPI00292950

SERPIND1

Serpin peptidase inhibitor, clade D (Heparin cofactor), member 1

0.17

0.28

− 1.581

IPI00296099

THBS1

Thrombospondin-1

0.08

0.12

− 1.506

  1. aAccession numbers of identified proteins were from the International Protein Index (IPI) Human database
  2. bHUGO gene symbols of mapped proteins were taken from the Ingenuity Pathways Analysis software
  3. cMol% of identified proteins was calculated using the exponentially modified protein abundance index (emPAI) value based on the number of identified peptides
  4. dFold change was calculated by dividing the protein’s mol% of PD 40 HDFs by protein’s mol% of passage #15 HDFs. If this number was less than 1, a negative sign was added to the reciprocal number. If the original fold change was calculated as 0.75, the negative sign of the calculated fold change was added to the reciprocal number, resulting in − 1.33. “passage #40” or “passage #15” indicates the exclusively identified protein in each group
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