Table I Numbers of distinct phosphopeptides and proteins that were identified and quantified in both biological replicates of EGF-stimulated Hela cells using iTRAQ and mTRAQ labeling
iTRAQiTRAQiTRAQbThresholdcmTRAQmTRAQmTRAQbThresholdciTRAQ ∩ mTRAQ
1212(p< 0.05)1212(p< 0.05)iTRAQmTRAQ
Phosphoproteomea
    identified pSTY-peptides20,87925,51513,74112,82213,5595,7964,0914,091
    identified proteins4,8515,5023,5914,8725,1832,6832,3032,303
    quantified pSTY-peptides:
    10min/0min19,38324,24112,129 [56%]d10,17712,1364,448 [40%]d2,9712,971
    ↑ regulated2,4763,9491,263 [10%]e0.702,4902,197538 [12%]e0.94323304
    ↓ regulated8081,311316 [3%]e−0.561,3161,416126 [3%]e−0.826980
    quantified pSTY-peptides:
    24h/0h19,42924,08512,311 [57%]d11,38510,9944,567 [41%]d3,1233,123
    ↑ regulated514592219 [2%]e1.631,143874138 [3%]e2.196583
    ↓ regulated23136081 [1%]e−1.1282884750 [1%]e−1.502425
    Proteomea
    identified peptides42,30948,19232,50725,79134,29118,05015,72715,727
    identified proteins4,4414,7113,4702,8823,1962,1871,9911,991
    quantified proteins:
    24h/0h3,3643,7442,699 [76%]d2,0802,1851,597 [75%]d1,4681,468
    ↑ regulated263614 [0.5%]e0.6517306 [0.4%]e1.34106
    ↓ regulated18309 [0.3%]e−0.6315185 [0.3%]e−1.2432
    Figures3A, 3B, 43A, 3B, 455
  • a All identified and quantified peptides/proteins are distinct.

  • b Quantified peptides/proteins are reproducible within a 99% prediction confidence interval based on linear regression.

  • c BH-FDR p value derived cut-off thresholds for regulated peptides are log2 transformed.

  • d Fraction of overlapping data between biological replicates in percent.

  • e Fraction of regulated peptides/proteins in percent.