Table 1.

GCF proteome, 199 proteins, documented for healthy periodondium sites.

Accession number	Protein name	^#	^§
Apoptosis and signal transduction
^SP31946	14-3-3 protein beta/alpha ^e	2	2
^SP31947	14-3-3 protein sigma^a ^b ^c ^d ^e	7	7
^SP63104	14-3-3 protein zeta/delta ^a ^b ^c ^e	6	7
^SP12814	Alpha-actinin-1 ^c ^e	2	2
O43707	Alpha-actinin-4 ^c ^e	2	2
^SP02647	Apolipoprotein A-I ^a ^b ^c ^d ^e	13	8
^SP02652	Apolipoprotein A-II ^b ^c ^e	3	4
^SP04114	Apolipoprotein B-100 ^a ^b ^d	3	5
^SP02649	Apolipoprotein E ^b ^d	4	3
^SO14791	Apolipoprotein-L1^b ^d	2	3
P54259	Atrophin-1 ^b	2	1
^SP23528	Cofilin-1^b ^e	3	4
P13569	Cystic fibrosis transmembrane conductance regulator ^a	2	1
^SP47929	Galectin-7 ^b ^e	2	3
P07900	Heat shock protein HSP 90-alpha^d ^e	2	2
Q5VST9	Obscurin ^a	3	2
Q8IV61	Ras guanyl-releasing protein 3 ^c	2	1
Q13114	TNF receptor-associated factor 3^d	2	1
Q7Z3T8	Zinc finger FYVE domain-containing protein 16 ^b ^c	2	2
Cytoskeleton structural proteins
^SP60709	Actin, cytoplasmic 1^a ^b ^c ^d ^e	7	7
^SP61158	Actin-related protein 3 ^d	3	1
P17661	Desmin ^b ^e	2	4
^SP15924	Desmoplakin ^e	2	3
^SP02751	Fibronectin ^d	2	3
^SP21333	Filamin-A ^a	2	1
^SP06396	Gelsolin ^b ^c ^d ^e	8	7
P78385	Keratin type II cuticular Hb3 ^e	2	1
O76013	Keratin, type I cuticular Ha6 ^b	2	2
^SP02533	Keratin, type I cytoskeletal 14 ^b	7	7
^SP08779	Keratin, type I cytoskeletal 16 ^b	5	6
^SP08727	Keratin, type I cytoskeletal 19 ^b	3	2
^SP35527	Keratin, type I cytoskeletal 9 ^c	3	11
P04264	Keratin, type II cytoskeletal 1^a ^c ^d	8	15
^SQ7Z794	Keratin, type II cytoskeletal 1b ^b ^e	2	6
^SP35908	Keratin, type II cytoskeletal 2 epidermal ^a ^b	4	12
Q01546	Keratin, type II cytoskeletal 2 oral^e	3	4
P12035	Keratin, type II cytoskeletal 3 ^e	2	3
P19013	Keratin, type II cytoskeletal 4 ^b	2	5
^SP13647	Keratin, type II cytoskeletal 5 ^a ^b	17	12
^SP02538	Keratin, type II cytoskeletal 6A ^a ^b ^c	22	10
^SP04259	Keratin, type II cytoskeletal 6B ^b	5	5
Q14CN4	Keratin, type II cytoskeletal 72 ^d	2	9
Q86Y46	Keratin, type II cytoskeletal 73 ^e	2	3
Q9UPN3	Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 ^c ^e	3	2
P11137	Microtubule-associated protein 2^e	2	10
^SP26038	Moesin ^b ^d ^e	2	3
P41219	Peripherin ^b	2	3
O15020	Spectrin beta chain, brain 2 ^e	2	1
^SQ9Y490	Talin-1 ^e	3	3
^SP08670	Vimentin ^b ^e	3	3
Extracellular structural and adhesion proteins
^SP01019	Angiotensinogen ^b ^c	2	2
P02461	Collagen alpha-1(III) chain ^a ^b	2	1
Q02388	Collagen alpha-1(VII) chain ^a ^b	2	2
Q99715	Collagen alpha-1(XII) chain ^a ^b	4	3
^SQ14993	Collagen alpha-1(XIX) chain ^b	3	1
P08123	Collagen alpha-2(I) chain ^a ^b	2	3
Q8N613	Cornulin ^b ^e	4	5
O60469	Down syndrome cell adhesion molecule^a	2	1
^SP02671	Fibrinogen alpha chain ^b ^c ^d ^e	10	4
^SP02675	Fibrinogen beta chain ^a ^b ^d	9	6
^SP02679	Fibrinogen gamma chain ^b	10	4
P13645	Keratin, type I cytoskeletal 10 ^a	4	9
^SP13646	Keratin, type I cytoskeletal 13 ^a	20	10
Q8WXI7	Mucin-16 ^e	4	2
Q5BJF6	Outer dense fiber protein 2 ^e	2	1
Q9BYM8	RanBP-type and C3HC4-type zinc finger-containing protein 1 ^b ^e	2	2
Q8IWN7	Retinitis pigmentosa 1-like1 protein^a	2	1
^SP02768	Serum albumin ^a ^b ^c ^d ^e	14	15
Q9UBC9	Small proline-rich protein 3 ^b ^e	7	6
^SQ4LDE5	Sushi, von Willebrand factor type A^a	3	4
Q9P2K2	Thioredoxin domain-containing protein 16 ^d	4	9
Q9BQ70	Transcription factor 25 ^a	2	1
P13611	Versican core protein ^b	2	1
^SP04004	Vitronectin ^b ^d	5	3
Hydrolytic enzymes
P49189	4-trimethylaminobutyraldehyde dehydrogenase ^d	2	2
P52209	6-phosphogluconate dehydrogenase, decarboxylating ^d ^e	3	3
^SP06733	Alpha-enolase ^b ^c ^d ^e	8	7
^SQ9NSC7	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1^b	2	1
Q6GMR7	Amidase domain containing protein^c	3	1
P08311	Cathepsin G ^b	3	3
^SP00450	Ceruloplasmin ^a ^b ^c	7	5
^SP04075	Fructose-bisphosphate aldolase A^d ^e	4	3
^SP04406	Glyceraldehyde-3-phosphate dehydrogenase ^d ^e	7	8
^SP00738	Haptoglobin ^b ^c	2	7
Q6ZRS2	Helicase SRCAP ^a	2	3
Q8TEK3	Histone-lysine N-methyltransferase, H3 lysine-79 specific ^b ^d	4	3
P08246	Leukocyte elastase ^b	2	5
^SP00338	L-lactate dehydrogenase A ^e	2	3
P43490	Nicotinamide phosphoribosyltransferase ^b	2	2
^SP00558	Phosphoglycerate kinase 1 ^d	2	1
^SP18669	Phosphoglycerate mutase 1 ^b ^c ^d ^e	3	9
^SP14618	Pyruvate kinase isozyme M1/M2^b ^d ^e	11	6
P55072	Transitional endoplasmic reticulum ATPase ^a	2	1
P29401	Transketolase ^c ^e	4	4
Q7Z410	Transmembrane protease, serine 9^d	2	1
^SP60174	Triosephosphate isomerase^e	2	1
Inflammatory and immune response
^SP04083	Annexin A1 ^a ^b ^d ^e	10	11
P06727	Apolipoprotein A-IV ^b	2	2
P17213	Bactericidal permeability- increasing protein ^b	2	1
^SP10909	Clusterin ^a ^b ^d ^e	4	6
^SP01024	Complement C3 ^a ^b ^c ^d ^e	27	9
^SP0C0L4	Complement C4-A ^d	7	2
^SP00751	Complement factor B ^b ^d	4	3
^SP31146	Coronin-1A ^e	2	2
^SP01876	Ig alpha-1 chain C region ^b ^c ^d ^e	2	6
^SP01857	Ig gamma-1 chain C region ^a ^b ^c ^d ^e	10	14
^SP01859	Ig gamma-2 chain C region ^a	6	7
^SP01861	Ig gamma-4 chain C region ^e	2	4
^SP01742	Ig heavy chain V-I region EU ^d	2	1
^SP01834	Ig kappa chain C region ^a ^b ^c ^d ^e	4	11
^SP01871	Ig mu chain C region ^b	2	2
^SP02788	Lactotransferrin ^a	2	5
^SP61626	Lysozyme C ^e	2	7
P05164	Myeloperoxidase ^e	2	1
^SP05109	Protein S100-A8 ^a	3	3
^SP06702	Protein S100-A9 ^a	2	2
^SP52566	Rho GDP-dissociation inhibitor 2 ^e	2	2
Intracellular protein/nucleotide binding
P62736	Actin, aortic smooth muscle ^a ^b ^c ^d ^e	15	13
Q562R1	Actin-like protein 2^d Alpha-1,6-mannosylglycoprotein 6-beta-	2	5
Q3V5L5	N-acetylglucosaminyltransferase B ^b	2	3
Q6S8J3	ANKRD26-like family C member 1A^a	11	11
Q9P2D7	Dynein heavy chain 1, axonemal ^a	2	3
^SP68104	Elongation factor 1-alpha 1^b ^e	5	3
P15311	Ezrin ^b ^d	2	2
^SP04792	Heat shock protein beta-1^b ^d ^e	6	9
^SP69905	Hemoglobin subunit alpha ^a ^b ^c ^d	2	8
^SP68871	Hemoglobin subunit beta ^a ^b ^c ^d	7	6
^SP02042	Hemoglobin subunit delta ^a ^b ^c ^d	2	1
^SP02790	Hemopexin ^a ^b ^d	7	3
^SP16403	Histone H1.2 ^e	2	1
P0C0S8	Histone H2A type 1 ^b ^e	3	7
Q96A08	Histone H2B type 1-A ^e	2	1
P33778	Histone H2B type 1-B ^b ^e	2	5
P68431	Histone H3.1^a ^b ^e	2	7
Q16695	Histone H3.1t ^b	3	1
^SP62805	Histone H4 ^a ^b ^c ^d ^e	6	10
Q5JU85	IQ motif and Sec7 domain-containing protein 2 ^d	2	1
Q96JM7	Lethal(3)malignant brain tumor-like 3 protein ^b	2	2
^SP40925	Malate dehydrogenase ^d	2	1
Q6P0Q8	Microtubule-associated serine/threonine-protein kinase 2 ^b	2	1
O14950	Myosin regulatory light chain MRLC2 ^b	2	1
P35580	Myosin-10 ^e	2	1
^SP35579	Myosin-9 ^b ^d ^e	6	5
Q14686	Nuclear receptor coactivator 6 ^b	2	1
P19338	Nucleolin ^d	2	1
P12755	Ski oncogene ^d	2	1
Q9P2P6	StAR-related lipid transfer protein 9^b ^c	2	2
Q92922	SWI/SNF complex subunit SMARCC1 ^a	2	2
Q86TI0	TBC1 domain family member 1 ^e	2	1
Q8TBP0	TBC1 domain family member 16 ^d	2	1
Q99973	Telomerase protein component 1 ^d	2	1
Q9BVT8	Transmembrane and ubiquitin- like domain-containing protein 1 ^a	2	2
Q71U36	Tubulin alpha-1A chain ^e	3	6
Q13748	Tubulin alpha-3C/D chain ^e	3	2
^SP68366	Tubulin alpha-4A chain ^b ^d ^e	3	4
^SQ13885	Tubulin beta- 2A chain ^e	3	4
O43309	Zinc finger and SCAN domain- containing protein 12 ^b	2	1
Protease/enzyme inhibitors
^SP01011	Alpha-1-antichymotrypsin ^d	2	1
^SP01009	Alpha-1-antitrypsin ^a	4	2
^SP01023	Alpha-2-macroglobulin ^a ^c ^d ^e	10	5
^SP07355	Annexin A2 ^b ^d ^e	5	4
P12429	Annexin ^e	2	4
^SP04080	Cystatin-B ^a	2	4
^SP05546	Heparin cofactor 2 ^d	2	1
^SP04196	Histidine-rich glycoprotein ^b	2
^SP19827	Inter-alpha-trypsin inhibitor heavy chain H1 ^d	6	1
^SP19823	Inter-alpha-trypsin inhibitor heavy chain H2 ^d	3	1
^SQ14624	Inter-alpha-trypsin inhibitor heavy chain H4 ^e	2	1
^SP30740	Leukocyte elastase inhibitor ^a	2	1
^SP30086	Phosphatidylethanolamine- binding protein 1 ^d	2	1
Proteins falling into various other categories
^SP11021	78 kDa glucose-regulated protein ^e	2	1
Q8WWM7	Ataxin-2-like protein ^d	2	1
Q9BXY5	Calcyphosin-2 ^d	2	1
^SP27482	Calmodulin-like protein 3 ^b ^e	2	5
Q8IV04	Carabin ^d	2	1
Q7Z7A1	Centriolin ^b	3	1
P35663	Cylicin-1 ^b	2	1
Q08477	Cytochrome P450 4F3 ^b	2	1
P06737	Glycogen phosphorylase ^d ^e	2	2
^SP34931	Heat shock 70 kDa protein 1L ^d ^e	2	5
P08238	Heat shock protein HSP 90-beta^b ^d ^e	2	1
Q9UHV7	Mediator of RNA polymerase II transcription subunit 13 ^b ^c	3	2
^SP62937	Peptidyl-prolyl cis-trans isomerase A ^b ^d ^e	3	3
^SP13796	Plastin-2 ^e	2	4
Q12809	Potassium voltage-gated channel subfamily H member 2 ^c	2	1
^SP07737	Profilin-1^e	3	6
^SP07237	Protein disulfide-isomerase ^e	2	1
^SP06703	Protein S100-A6 ^e	2	2
P46940	Ras GTPase-activating-like protein ^d	3	1
P21817	Ryanodine receptor 1 ^e	2	2
^SP02787	Serotransferrin ^a	2	6
^SP27169	Serum paraoxonase/arylesterase 1^b	2	4
Q99536	Synaptic vesicle membrane protein VAT-1^b	2	1
^SQ8WZ42	Titin ^a ^b ^d	47	10
^SP02766	Transthyretin ^a	3	2
^SP02774	Vitamin D-binding protein ^c	2	1
Q96KN7	X-linked retinitis pigmentosa GTPase regulator ^b	2	1
Q9H2Y7	Zinc finger protein 106 homolog ^e	2	1
^SQ96DA0	Zymogen granule protein 16 homolog B ^b	3	5

The proteins have been grouped into seven different categories based on their known biological function(s). The superscript capital “S” on the left of accession numbers denotes proteins that can be also identified in plasma proteome [22] by MS analysis. Blue color highlights group category. The small superscript letters on the right of protein names denotes;

proteins identified by electroelution using SDS-PAGE, dissected sections, in gel digested and analyzed by LC-MS/MS,

proteins remaining on the periopaper after elution with ammonium bicarbonate,

proteins remaining on the SwellGel blue,

GCF sample after albumin removal of proteins eluted from the SwellGel blue,

direct analysis of the proteins eluted with ammonium bicarbonate 50 mM pH 8.0 without any fractionation step or number of times each protein identified albumin removal. Symbols;

refer to number of peptides of each protein identified, and

^§

refer to number of times each protein identified.