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Table 2 Expected ratios and computed ratios for seven proteins in standard mixtures

From: High-throughput peptide quantification using mTRAQ reagent triplex

(a) Set1 experiment

Protein

Number of MS/MS

M/L

H/L

Expected ratio

Our ratio

Standard deviation

Expected ratio

Our ratio

Standard deviation

  

LALBA

17

1

1.074858

0.085456

1

0.695681

0.072863

CSN2

3

2

4.847636

0.093352

0.2

0.184493

0.045277

TF

76

0.1

0.098397

0.186558

0.3

0.160631

0.141608

CSN1S1

10

1

1.264178

0.10274

3

1.948002

0.085701

CSN1S2

4

1

2.419368

0.133448

3

1.644656

0.088651

CYCS

15

1

0.846116

0.068538

0.3

0.34976

0.123581

LGB

22

5

5.138141

0.181286

10

8.143161

0.174779

(b) Set2 experiment

Protein

Number of MS/MS

M/L

H/L

Expected ratio

Our ratio

Standard deviation

Expected ratio

Our ratio

Standard deviation

  

LALBA

18

1

1.010655

0.098869

1

0.487596

0.076048

CSN2

3

10

13.64935

0.112667

5

1.517403

0.112521

TF

64

0.33

0.43843

0.166834

3.3

2.829079

0.108205

CSN1S1

13

0.33

0.471544

0.071577

0.33

0.223681

0.084549

CSN1S2

10

0.33

0.984124

0.042867

0.33

0.274309

0.083823

CYCS

13

3

1.83768

0.049094

3

1.417869

0.083364

LGB

18

0.5

0.436385

0.049273

0.1

0.050817

0.220646

  1. We first calculated the averages and standard deviations of log10(H/L) values of peptides. Then, we transformed the averages into H/L scale to compare them to expected ratios.