Details

Autor(en) / Beteiligte

• Colinge, Jacques
• Chiappe, Diego
• Lagache, Sophie
• Moniatte, Marc
• Bougueleret, Lydie

Titel

Differential Proteomics via Probabilistic Peptide Identification Scores

Ist Teil von

• Analytical chemistry (Washington), 2005-01, Vol.77 (2), p.596-606

Ort / Verlag

Washington, DC: American Chemical Society

Erscheinungsjahr

2005

Quelle

MEDLINE

Beschreibungen/Notizen

• Relative quantitation is key to enable differential proteomics and hence answer biological questions by comparing samples. Classical approaches involve stable isotope labeling with/without spiked standards. Although stable isotopes may lead to precise results, their application is not straightforward. In Proteomics, 2004, 4, 2333−2351, we proposed an approach where we summed peptide identification scores to derive a semiquantitative abundance indicator. In this study, we combine such an indicator with a statistical test to detect differentially expressed proteins. We demonstrate the effectiveness of this method by using mixtures of purified proteins and human plasma spiked with proteins at low-nanomolar concentrations. The impact of the number of repeated experiments is discussed, and we show that the statistical test we use performs well with two to three repetitions, whereas a classical t-test would require at least four repetitions to achieve the same performance. Typically, 2.5−5-fold changes are detected with 90−95% confidence in human plasma. The method is finally characterized by deriving estimates of its false positive and negative rates. This new characterization is valid for a wider class of methods such as spectrum sampling (Liu, H.; Sadygov, R. G.; Yates, J. R. III. Anal. Chem. 2004, 76, 4193−4201).