n vitro bioassembled human extracellular matrix and its application in human embryonic stem cell cultivation 2

46




DxSDOC
DxSDOCDOC
Subcellular
Location
Accession #
Molecular
Weight
(Da)
Protein Name
Identification
Probability
# of
Unique
Peptides
%
Coverage
Protein name
Identification
Probability
# of
Unique
Peptides
%
Coverage
Cytoplasm

IPI00216587,
IPI00645201
24188
40S ribosomal protein
S8*
100.00%
3
18.80%
40S ribosomal protein
S8*
99.80%
2
13.50%

IPI00021439,
IPI00894365,
IPI00894498
41720
Actin, cytoplasmic 1*
100.00%
6
28.30%
Actin, cytoplasmic 1*
100.00%
9
36.50%

IPI00025416
41860
Actin, gamma-enteric

smooth muscle*
99.80%
2
17.30%





IPI00013452
170575
Bifunctional aminoacyl-
tRNA synthetase*
99.80%
2
2.18%





IPI00152692
23406
D-tyrosyl-tRNA(Tyr)
deacylase 1
99.80%
2
14.80%
D-tyrosyl-tRNA(Tyr)
deacylase 1

99.80%
2
14.80%

IPI00396485,
IPI00472724
50123
Elongation factor 1-
alpha 1*
100.00%
4
14.30%
Elongation factor 1-
alpha 1*
99.80%
2
5.63%

IPI00297982
51092
Eukaryotic translation
initiation factor 2
subunit 3
99.80%
2
7.20%

IPI00219018,
IPI00789134,
IPI00795257
36035
Glyceraldehyde-3-
phosphate
dehydrogenase*
†

100.00%
4
20.00%
Glyceraldehyde-3-
phosphate
dehydrogenase*
†

99.80%
2
8.66%

IPI00414676
83249
Heat shock protein HSP
90-beta*
99.80%
2
5.25%

IPI00141318,
IPI00604713,
IPI00883950,
IPI00939370
66004
Isoform 1 of
Cytoskeleton-associated
protein 4*
†

100.00%
7
16.30%
Isoform 1 of
Cytoskeleton-
associated protein 4*
†

99.80%
2
4.82%

IPI00003865,
IPI00037070,
IPI00939595
70882

Isoform 1 of Heat shock
cognate 71 kDa
protein*
†

100.00%
4
9.13%





47

IPI00019502
226520
Isoform 1 of Myosin-9*
100.00%
16
12.90%
Isoform 1 of Myosin-
9*
†

100.00%
3
2.81%

IPI00302592,

IPI00333541,
IPI00644576
279991
Isoform 2 of Filamin-A*
100.00%
14
8.72%
Isoform 2 of Filamin-
A*
100.00%
2
1.10%

IPI00043863,
IPI00220113,
IPI00396171,
IPI00411375,
IPI00743873,
IPI00878314,
IPI00878651,
IPI00880007,
IPI00888475,
IPI00924603,
IPI00927173,
IPI00927819
88260
Isoform 3 of
Microtubule-associated
protein 4
100.00%

3
5.19%





IPI00465248,
IPI00759806
47152
Isoform alpha-enolase of
Alpha-enolase*
99.80%
2
6.68%





IPI00479186,
IPI00847989
57920
Isoform M2 of Pyruvate
kinase isozymes
M1/M2*
99.80%
2
6.59%

IPI00000105,
IPI00910019
99308
Major vault protein*
†

100.00%
4
10.10%





IPI00008868
270602
Microtubule-associated
protein 1B*
†

100.00%
3
3.04%

IPI00166768,
IPI00180675,
IPI00218343,
IPI00387144,
IPI00792677,
IPI00793930,
IPI00909762,
IPI00930688
36725
TUBA1C protein
99.80%
2
10.10%





IPI00418471
53635
Vimentin*
100.00%
3
11.60%

IPI00215743,
152453




Isoform 3 of
100.00%
3
3.33%

48
IPI00220967,
IPI00744135,
IPI00856098
Ribosome-binding
protein 1

IPI00009865
58811




Keratin, type I
cytoskeletal 10
100.00%
2
5.31%

IPI00220327
66022




Keratin, type II
cytoskeletal 1
99.80%
2
3.42%
Extracellular
Matrix
IPI00297646
138923
Collagen alpha-1(I)
chain*
†

100.00%
4
4.10%
Collagen alpha-1(I)
chain*
†

100.00%
5
5.74%

IPI00304962
129297
Collagen alpha-2(I)
chain*
†

100.00%
7
8.57%
Collagen alpha-2(I)
chain*
†

100.00%
5
5.49%

IPI00013079
106649
EMILIN-1*
†

100.00%
5
8.17%
EMILIN-1*
†

100.00%

4
6.40%

IPI00328113
312268
Fibrillin-1*
100.00%
3
1.25%
Fibrillin-1*
99.80%
2
0.94%

IPI00329573,
IPI00964552
333127
Isoform 1 of Collagen
alpha-1(XII) chain
100.00%
23
11.80%
Isoform 1 of Collagen
alpha-1(XII) chain
100.00%
21
10.10%

IPI00022200,
IPI00072918,

IPI00220701
343645
Isoform 1 of Collagen
alpha-3(VI) chain*
†

100.00%
15
7.84%
Isoform 1 of Collagen
alpha-3(VI) chain*
†

100.00%
10
5.23%

IPI00022418,
IPI00339223,
IPI00339224,
IPI00339225,
IPI00339226,
IPI00339227,
IPI00845263,
IPI00855785
262599
Isoform 1 of
Fibronectin*
†

100.00%
21
14.60%
Isoform 1 of
Fibronectin*
†

100.00%
15
8.51%

IPI00031008,
IPI00220213
240832
Isoform 1 of Tenascin*
†

100.00%
8
5.77%
Isoform 1 of
Tenascin*
†

100.00%
7
4.54%

IPI00294578
77311

Isoform 1 of
Transglutaminase 2
100.00%
5
12.40%
Isoform 1 of
Transglutaminase 2
100.00%
4
10.50%

IPI00304840
108563
Isoform 2C2 of Collagen
alpha-2(VI) chain
99.80%
2
4.61%





IPI00296099
129364
Thrombospondin-1*
100.00%
7
8.29%
Thrombospondin-1*

100.00%
6
6.50%

IPI00298971
54288
Vitronectin*
99.80%
2
8.79%





IPI00005908
105340




A disintegrin and
100.00%
3
4.96%

49
metalloproteinase with
thrombospondin
motifs 1*

†


IPI00018219,
IPI00873923,
IPI00940091
74665




Transforming growth
factor-beta-induced
protein ig-h3
100.00%
2
4.69%
Membrane
IPI00022143,
IPI00746655
122841
Isoform 1 of Extended
synaptotagmin-1*
†

99.80%
2
2.54%

IPI00021048,
IPI00216268,
IPI00216269,
IPI00645867
234698
Isoform 1 of
Myoferlin*
†

100.00%
3
1.89%





IPI00219365,
IPI00872814
67804
Moesin*
100.00%
3
7.45%

Nucleus
IPI00217466
22333
Histone H1.3
100.00%
3
14.50%
Histone H1.3
100.00%
3
17.60%

IPI00217468
22564
Histone H1.5
100.00%
3
14.20%
Histone H1.5
100.00%
3
13.70%

IPI00021924
22470
Histone H1x*
99.80%
2
14.10%

IPI00021405,
IPI00216952,
IPI00644087,
IPI00655812
74123
Isoform A of Prelamin-
A/C
100.00%
6
11.30%
Isoform A of
Prelamin-A/C
100.00%
5
9.04%

IPI00021812
629086
Neuroblast
differentiation-
associated protein
AHNAK*
†

100.00%

9
2.36%





IPI00646304
23725
Peptidyl-prolyl cis-trans
isomerase B*
†

99.80%
2
12.00%





IPI00018534,
IPI00020101,
IPI00152906,
IPI00303133,
IPI00329665,
IPI00419833,
IPI00477495,
IPI00554798,
IPI00646240,

13935




Histone H2B type 1-L
99.90%
2
20.60%

50
IPI00794461,
IPI00815755,
IPI00930174,
IPI00930570
Unknown
IPI00022431,
IPI00795830,
IPI00922262,
IPI00953689
46608
cDNA FLJ55606, highly
similar to Alpha-2-HS-
glycoprotein
99.80%
2
3.00%
cDNA FLJ55606,
highly similar to
Alpha-2-HS-

glycoprotein
99.80%
2
3.00%

IPI00376689
152983
Isoform 1 of Protein
KIAA1199
99.80%
2
1.91%





IPI00022434,
IPI00745872,
IPI00966829
71687
Putative uncharacterized
protein ALB
100.00%
3
7.02%
Putative
uncharacterized
protein ALB
100.00%

3
7.81%
Table 2: Consolidated list of protein identifications compiled from mass spectrometric analysis of DxSDOC and DxSDOCDOC matrices. Mass
spectrometry analysis was done in collaboration with Christopher Stephen Hughes and Prof Gilles Lajoie.
* Protein also found in GFR and standard Matrigel, based on work by Hughes et. al. 2009.
†
Murine protein is a homolog of human protein