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Table 1 List of unique proteins identified in AH surgery samples.

From: Analysis of protein composition of rabbit aqueous humor following two different cataract surgery incision procedures using 2-DE and LC-MS/MS

Protein name

Accession #

Protein typea

Surgery typeb

Found in [19] ?

# of peptidesc

Peptide sequenced

Peptide charged

PIP [%]e

Serum albumin [O. cuniculus]1,2,3,4

gi|126723746

S

C, L

yes

27

  

100

Serum albumin [B. taurus]1

gi|1351907

S

C, L

yes

3

  

100

Albumin [M. mulatta]1

gi|109074537

S

C, L

yes

2

  

100

ALB protein [H. sapiens]

gi|25058739

S

L

yes

3

  

100

SLAM family member 9 [H. sapiens]1,2,3,4

gi|74760694

C

C, L

no

1

LATVVPEK

2

95

Apolipoprotein A-I [O. cuniculus]1,2

gi|83628258

S

C, L

yes

14

  

100

Alpha-1-antiproteinase F [O. cuniculus]1,2

gi|126722912

S

C, L

yes

7

  

100

Serum Transferrin Chain A [O. cuniculus]1,2,3

gi|15825992

S

C, L

yes

16

  

100

Tudor domain-containing protein 12 [M. musculus]1,2,3

gi|162416223

C

C, L

no

1

SPLSADLKK

2

95

Iodotyrosine dehalogenase 1 protein [M. musculus]1,2

gi|21312562

C

C, L

no

1

DATVPDLK

2

94

Histidine-rich glycoprotein [O. cuniculus]1

gi|2494026

S

C

yes

3

  

100

Pancortin 1 [P. troglodytes]1

gi|55632585

C

C, L

no

1

DASLLSPR

2

94

Try10-like trypsinogen [M. musculus]1,2

gi|51092303

S

C

yes

1

TLDNDIMLIK

2

95

Paraoxonase [O. cuniculus]1,2

gi|126722853

S

C, L

no

1

NPPASEVLR

2

95

Mitogen-activated protein kinase 4 [R. norvegicus]1

gi|157819181

C

C, L

no

1

SHSFSDPSPK

2

94

Mucin 16 [H. sapiens]1

gi|34501467

C

C

no

1

LSTSPIK

2

 

DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 [M. musculus]1

gi|109734461

C

C

no

1

AMALADR

2

95

Ribosomal protein L24 [M. musculus]1,3

gi|94390118

C

C, L

no

1

AAPKQKIVK

1

95

Alpha-2-HS-glycoprotein [O. cuniculus]1,2

gi|12644357

S

C, L

yes

3

  

100

Gamma-fibrinogen chain fragment [H. sapiens]

gi|577055

S

C, L

yes

2

  

100

Programmed cell death 8 [M. mulatta]1

gi|109132217

C

C

no

1

LLIKLKDGR

2

94

FERM [C. familiaris]1,3

gi|73994333

C

C, L

no

1

ALTADLPR

2

95

tRNA wybutosine-synthesizing protein 2 [R. norvegicus]1

gi|143679922

C

C

no

1

VAVVAEPR

2

95

Adenylate cyclase 6 [M. musculus]1

gi|148672233

C

C, L

yes

1

GKEEKAMLAK

1

94

Actin, cytoplasmic 1 (Beta-actin) [O. cuniculus]1

gi|231506

C

C, L

yes

2

  

100

HIST2H3C protein [P. troglodytes]

gi|55626038

C

L

yes

6

  

100

Vitamin D-binding protein [O. cuniculus]1

gi|603499

C

C, L

yes

2

  

100

Formin-1 (Limb deformity protein) [M. musculus]1

gi|158518557

C

C, L

no

1

IIKLLDGKR

2

93

Immunoglobulin kappa chain [O. cuniculus]1

gi|1100745

S

L

no

1

VTQGTTSVVQSFNR

2

95

Cytochrome P450, family 2, polypeptide 66 [R. norvegicus]1,2

gi|109463861

C

L

no

1

CLVDELR

2

92

E2F transcription factor 4 [M. mulatta]1,4

gi|109128874

C

L

no

1

LAADTLAVR

2

92

Protein arginine N-methyltransferase 5 [M. musculus]1

gi|32171623

C

C, L

no

1

GITLSVRP

1

93

Alpha-1-antiproteinase E [O. cuniculus]

gi|126722876

S

L

yes

4

  

100

Preproalbumin [C. porcellus]1,2

gi|33518896

S

L

no

2

  

100

Tubulin beta-2A chain [R. norvegicus]

gi|116242815

C

L

no

6

  

100

The Structure Of Collagen Type I Chain A [R. norvegicus]

gi|109156929

C

L

no

2

  

100

Eukaryotic translation elongation factor 1 [M. mulatta]

gi|109071712

C

L

no

2

  

100

Desmoplakin [B. taurus]

gi|76651410

C

L

yes

3

  

100

Desmoplakin [R. norvegicus]

gi|10950477841

C

C

yes

2

  

99

Stratifin [M. mulatta]

gi|108999776

C

L

no

3

  

100

Gelsolin [M. mulatta]

gi|109110365

C

L

no

3

  

100

Transthyretin [O. cuniculus]2

gi|136466

S

C, L

yes

2

  

100

Junction plakoglobin [M. mulatta]

gi|109115422

C

C, L

yes

2

  

100

Hemopexin [O. cuniculus]

gi|1070649

S

C, L

yes

2

  

99

Complement C3 [C. potcellus]

gi|544053

S

L

yes

2

   

Desmoglein 4 [M. musculus]

gi|148664532

C

C, L

yes

2

   

Dermcidin preproprotein [M. mulatta]

gi|109096991

S

L

yes

2

  

100

Cytosolic sialic acid 9-O-acetylesterase [C. familiaris]

gi|73954581

C

C, L

no

1

MELLADK

2

95

SK2 [C. familiaris]1

gi|73970454

C

C, L

no

1

IVTVETK

2

90

Platelet-activating factor acetylhydrolase [C. porcellus]

gi|2497686

S

C, L

no

1

WNSPLK

2

93

Filaggrin 2 [H. sapiens]1

gi|74755309

C

C, L

no

1

FSNSSSSNEFSK

2

94

Shank-interacting protein-like 1 [C. familiaris]1

gi|73974864

C

C, L

no

1

WAALVR

2

94

Collagen, Alpha 3 type VI [C. familiaris]1

gi|73990557

C

C, L

no

1

GVSGDRGSK

1

88

Valosin-containing protein [H. sapiens]1

gi|11095436

C

C

no

1

GDIFLVR

1

83

Plasminogen [H. sapiens]1

gi|38051823

S

C, L

yes

1

EAQLPVIENK

2

91

Sterol O-acyltransferase 1 [R. norvegicus]1

gi|13592087

C

C

no

1

QRCPLK

2

93

Peroxisomal membrane protein 2 [B. taurus]1

gi|114050981

C

C

no

1

APAASKLR

2

95

Isocitrate dehydrogenase 3 (NAD+) gamma [H. sapiens]1

gi|12804901

C

C

no

1

VATVAGSAAK

2

88

HEJ1 [H. sapiens]1

gi|14719299

C

C, L

no

1

EQYSAVIIAK

2

94

Olfactory receptor Olr1474 [R. norvegicus]1

gi|47575923

C

C

no

1

DMKDALIR

2

95

Bloom syndrome protein [M. mulatta]1

gi|109082375

C

C, L

no

1

LFKKLILDK

1

88

Methylmalonyl-CoA mutase [B. taurus]1

gi|11544644

C

L

no

1

KVKSSR

1

85

Cationic trypsin-3 [R. norvegicus]1

gi|136417

S

C, L

no

2

  

89

Limbin [C. familiaris]1

gi|73951860

C

L

no

1

LASYLSR

2

89

AMMECR1 [H. sapiens]

gi|6063689

?

L

no

1

MAAGCCGVKK

2

85

Olfactory receptor, family 2, member 35 [H. sapiens]1

gi|49226830

C

C, L

no

1

VATVIRKG

2

86

DmX-like protein 2 (Rabconnectin-3) [M. musculus]1

gi|90109865

C

L

no

1

HTKASSKQPLR

2

88

Aristaless 3 [C. familiaris]1

gi|73959917

C

L

no

1

AWGPACGPKLPR

2

82

Lamin B receptor variant [H. sapiens]

gi|62088608

C

C, L

no

1

KMPSRK

2

91

Zipper CG15792-PA [M. mulatta]

gi|109071904

C

C, L

no

1

AESGNPSIQQKIR

2

87

Kallikrein 24 [M. musculus]

gi|8393675

S

C, L

no

1

DKSNDLMLLR

2

87

GTP-binding protein Mx2 [C. familiaris]

gi|7271909

C

C

no

1

LIEGEEIVKK

2

90

Alpha-1-acid glycoprotein [O. cuniculus]

gi|112880

S

L

yes

1

NSVADLLLLR

2

94

Lumican [O. cuniculus]

gi|21542114

S

L

no

1

FNGLQYLR

2

94

Annexin A1 [O. cuniculus]

gi|1703316

C

L

no

1

TPAQFDADELR

2

94

Complement component 8, gamma [O. cuniculus]

gi|126722836

S

L

no

1

YGATGVPGR

2

91

Serotransferrin [O. cuniculus]

gi|6175087

S

C

no

1

VPSXAVVAR

2

92

Crystallin, lambda 1 [O. cuniculus]

gi|126723698

C

C

no

1

QITGALENIR

2

94

Alpha-2-plasmin inhibitor [O. cuniculus]

gi|130488651

S

C

no

1

SKFDPSLTQR

2

96

Ig gamma heavy chain constant region [O. cuniculus]

gi|2136983

S

L

no

1

VYTMGPPR

2

90

  1. aProtein type: S - serum protein, C - cellular protein, ? - not determined (as found in protein databases)
  2. bSurgery type: C - clear corneal incision, L - limbal incision
  3. cHighest number of different peptides in gel spot(s) for corresponding protein if found in multiple gel spots
  4. dPeptide sequence and peptide charge are given for 1 peptide if identified in multiple gel spots of clear corneal and/or limbal surgery. As well, 1 peptide hits were multiple observed (multiple MS spectra in one spot) in several individual spots.
  5. eProtein identification probability (PIP) as given by Scaffold software; if protein was identified in multiple spots only highest protein probability is listed in Table 1.
  6. 1identified in multiple gel spots within the same surgery type (clear corneal or limbal incision)
  7. 2identified in the same spot during different time points within the same type of surgery
  8. 3identified in the same spot of different type of surgery (clear corneal vs limbal incision)
  9. 4identified in the same spot of the same type of surgery in both low and high protein load (low vs high)
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