Table 1.
Protein-bound proteins that were found to be common to at least two cysts
| IPI number | Common name of protein | TPP confidence | Number of matching peptides | Percent coverage (%) |
|---|---|---|---|---|
| IPI00745872 | Serum ALB precursor, isoform 1* | 1.0000 | 94 | 75.0 |
| IPI00298828 | β-2-glycoprotein 1 precursor* | 1.0000 | 18 | 47.8 |
| IPI00816555 | IGLV2-14 protein* | 1.0000 | 2 | 46.2 |
| IPI00022488 | Hemopexin precursor* | 1.0000 | 21 | 45.5 |
| IPI00014048 | Ribonuclease pancreatic precursor* | 1.0000 | 3 | 43.6 |
| IPI00845354 | IGKC protein* | 1.0000 | 10 | 40.6 |
| IPI00430808 | Immunoglobulin light chain* | 1.0000 | 6 | 37.0 |
| IPI00784985 | Putative uncharacterized protein* | 1.0000 | 6 | 37.0 |
| IPI00026314 | Gelsolin precursor, isoform 1* | 1.0000 | 20 | 35.7 |
| IPI00021841 | APO A1 precursor* | 1.0000 | 7 | 33.5 |
| IPI00019580 | PLG precursor* | 1.0000 | 16 | 33.3 |
| IPI00399007 | Putative uncharacterized protein DKFZp686I04196* | 1.0000 | 15 | 32.9 |
| IPI00472345 | IGHG3 protein* | 1.0000 | 8 | 31.3 |
| IPI00006114 | PEDF precursor* | 1.0000 | 11 | 26.8 |
| IPI00165972 | Complement factor D preproprotein* | 1.0000 | 4 | 20.4 |
| IPI00032293 | Cystatin-C precursor* | 1.0000 | 3 | 19.2 |
| IPI00377087 | Gelsolin precursor, isoform 2+ | 1.0000 | 2 | 18.6 |
| IPI00022371 | Histidine-rich glycoprotein precursor* | 1.0000 | 6 | 17.0 |
| IPI00019581 | Coagulation factor XII precursor* | 1.0000 | 6 | 16.8 |
| IPI00011264 | Complement factor H-related protein 1 precursor* | 1.0000 | 4 | 16.7 |
| IPI00152331 | Metastasis suppressor protein 1, isoform 1§ | 0.9702 | 1 | 15.2 |
| IPI00829877 | IGL@ protein* | 1.0000 | 2 | 15.0 |
| IPI00022420 | Plasma retinol-binding protein precursor* | 1.0000 | 2 | 12.1 |
| IPI00022426 | AMBP protein precursor* | 1.0000 | 3 | 11.1 |
| IPI00019591 | Complement factor B precursor (Fragment), isoform 1* | 1.0000 | 5 | 10.7 |
| IPI00032328 | HMW of Kininogen-1 precursor, isoform+ | 1.0000 | 2 | 10.3 |
| IPI00021885 | Fibrinogen α-chain precursor, isoform 1* | 1.0000 | 6 | 9.9 |
| IPI00218508 | Complement factor B precursor (Fragment), isoform 2+ | 1.0000 | 3 | 9.7 |
| IPI00029739 | Complement factor H precursor, isoform 1+ | 1.0000 | 7 | 9.4 |
| IPI00011252 | Complement component C8 α-chain precursor§ | 1.0000 | 3 | 7.7 |
| IPI00294395 | Complement component C8 β-chain precursor+ | 1.0000 | 3 | 6.9 |
| IPI00218999 | Complement factor H precursor, isoform 2§ | 1.0000 | 3 | 6.9 |
| IPI00021145 | Dual specificity protein phosphatase CDC14A, isoform 1+ | 0.9963 | 1 | 6.6 |
| IPI00022431 | α-2-HS-glycoprotein precursor* | 0.9999 | 1 | 5.4 |
| IPI00032179 | Antithrombin III variant* | 0.9956 | 1 | 5.4 |
| IPI00009865 | Keratin, type I cytoskeletal 10§ | 1.0000 | 2 | 4.7 |
| IPI00555812 | Vitamin D-binding protein precursor* | 1.0000 | 2 | 4.6 |
| IPI00220327 | Keratin, type II cytoskeletal 1+ | 0.9997 | 2 | 4.3 |
| IPI00296608 | Complement component C7 precursor§ | 1.0000 | 1 | 3.1 |
| IPI00299568 | Cytochrome P450 2A6+ | 0.9993 | 2 | 2.9 |
| IPI00019568 | Prothrombin precursor (Fragment)+ | 1.0000 | 1 | 2.7 |
| IPI00553177 | α-1-Antitrypsin precursor* | 0.9865 | 1 | 2.2 |
| IPI00783987 | Complement C3 precursor (Fragment)* | 0.9447 | 1 | 1.3 |
| IPI00784368 | Glucosaminyl N-deacetylase/N-sulfotransferase§ | 0.9746 | 1 | 0.8 |
Proteins identified only in the biomarker enriched samples versus depleted cyst fluid results from our prior experiment [2] are in bold font. Common names of proteins are followed by a symbol to recognize the number of cysts the protein was identified in: 4/4 cysts (*), 3/4 cysts (+) and 2/4 cysts (§). Each protein is distinct, meaning that each identified protein had at least one unique peptide. Peptides and proteins were identified by SEQUEST and validated via the TPP via PeptideProphet and ProteinProphet. Only those identified with > 90% confidence is listed. IPI accession numbers are linked to the common names.