Table 1.
List of six normalizing proteins and eighteen target proteins of interest
| Protein (HUMAN) | Protein name | Concentration a (ng/ml) | Transition b (peptide_Q1_Q3) | FDR c | F n d |
e
|
Ă n f |
|---|---|---|---|---|---|---|---|
| Normalizing proteins | |||||||
| PEDF | Pigment epithelium-derived factor | 7200 | LQSLFDSPDFSK_692.34_593.30 | 1.40E-04 | 0.971 | 1.756 | 1.209E06 |
| MASP1 | Mannan-binding lectin serine protease 1 | 240 | TGVITSPDFPNPYPK_816.92_258.10 | 5.75E-04 | 0.957 | 0.360 | 1.060E05 |
| GELS | Gelsolin | 16000 | TASDFITK_441.73_710.40 | 3.18E-04 | 0.852 | 0.502 | 1.897E06 |
| LUM | Lumican | 4000 | SLEDLQLTHNK_433.23_499.30 | 3.82E-04 | 0.838 | 10.846 | 4.717E06 |
| C163A | Scavenger receptor cysteine-rich type 1 protein M130 | 94 | INPASLDK_429.24_630.30 | 1.19E-03 | 0.823 | 0.392 | 4.690E04 |
| PTPRJ | Receptor-type tyrosine-protein phosphatase eta | 9.9 | VITEPIPVSDLR_669.89_896.50 | 1.44E-03 | 0.926 | 0.275 | 4.685E04 |
| Target proteins of interest | |||||||
| AIFM1 | Apoptosis-inducing factor 1, mitochondrial | 1.4 | ELWFSDDPNVTK_725.85_558.30 | 3.70E-02 | Assay specificity not verified | ||
| KIT | Mast/stem cell growth factor receptor | 8.2 | YVSELHLTR_373.21_428.30 | 2.40E-03 | 0.730 | ||
| FRIL | Ferritin light chain | 12 | LGGPEAGLGEYLFER_804.40_1083.60 | 4.30E-05 | 0.844 | ||
| LRP1 | Prolow-density lipoprotein receptor-related protein 1 | 20 | TVLWPNGLSLDIPAGR_855.00_1209.70 | 1.40E-04 | Assay specificity not verified | ||
| COIA1 | Collagen alpha-1(XVIII) chain | 35 | AVGLAGTFR_446.26_721.40 | 6.70E-04 | 0.732 | ||
| PRDX1 | Peroxiredoxin-1 | 60 | QITVNDLPVGR_606.30_970.50 | 1.90E-05 | 1.714 | ||
| TENX | Tenascin-X | 70 | YEVTVVSVR_526.29_293.10 | 1.10E-03 | 0.699 | ||
| ENPL | Endoplasmin | 88 | SGYLLPDTK_497.27_308.10 | 1.10E-03 | 0.649 | ||
| GRP78 | 78 kDa glucose-regulated protein | 100 | TWNDPSVQQDIK_715.85_288.10 | 1.80E-03 | 1.140 | ||
| BGH3 | Transforming growth factor-beta-induced protein ig-h3 | 140 | LTLLAPLNSVFK_658.40_804.50 | 1.40E-04 | 0.779 | ||
| ALDOA | Fructose-bisphosphate aldolase A | 250 | ALQASALK_401.25_617.40 | 3.70E-05 | 0.777 | ||
| GGH | Gamma-glutamyl hydrolase | 250 | YYIAASYVK_539.28_638.40 | 1.70E-03 | 0.834 | ||
| CD14 | Monocyte differentiation antigen CD14 | 420 | ATVNPSAPR_456.80_527.30 | 4.30E-04 | 0.789 | ||
| LG3BP | Galectin-3-binding protein | 440 | VEIFYR_413.73_598.30 | 2.80E-05 | 0.842 | ||
| TSP1 | Thrombospondin-1 | 510 | GFLLLASLR_495.31_559.40 | 1.90E-05 | 0.625 | ||
| IBP3 | Insulin-like growth factor-binding protein 3 | 5700 | FLNVLSPR_473.28_685.40 | 2.80E-05 | 0.790 | ||
| TETN | Tetranectin | 58000 | LDTLAQEVALLK_657.39_871.50 | 3.70E-05 | 0.760 | ||
| ISLR | Immunoglobulin superfamily containing leucine-rich repeat protein | ALPGTPVASSQPR_640.85_841.50 | 4.40E-03 | 0.850 | |||
aPredicted plasma concentration
[26]. bThe transition that was used for quantification. cFalse discovery rate for peptide MRM assay (peptide Q value)
[6]. dCorrection factor {F
n} in Study II in which a new lot of SIS peptides were used. eScaling constant
for InteQuan. fScaling constant {Ă
n} for EPN