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Table 1 List of six normalizing proteins and eighteen target proteins of interest

From: An integrated quantification method to increase the precision, robustness, and resolution of protein measurement in human plasma samples

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   
  1. 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