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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

Ä‚ 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 {Ä‚ n } for EPN
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Clinical Proteomics

ISSN: 1559-0275