pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios

详细信息    查看全文

• 作者：Chao Liu ; Chun-Qing Song ; Zuo-Fei Yuan ; Yan Fu ; Hao Chi ; Le-Heng Wang ; Sheng-Bo Fan ; Kun Zhang ; Wen-Feng Zeng ; Si-Min He ; Meng-Qiu Dong ; Rui-Xiang Sun
• 刊名：Analytical Chemistry
• 出版年：2014
• 出版时间：June 3, 2014
• 年：2014
• 卷：86
• 期：11
• 页码：5286-5294
• 全文大小：350K
• 年卷期：v.86,no.11(June 3, 2014)
• ISSN：1520-6882

文摘

In relative protein abundance determination from peptide intensities recorded in full mass scans, a major complication that affects quantitation accuracy is signal interference from coeluting ions of similar m/z values. Here, we present pQuant, a quantitation software tool that solves this problem. pQuant detects interference signals, identifies for each peptide a pair of least interfered isotopic chromatograms: one for the light and one for the heavy isotope-labeled peptide. On the basis of these isotopic pairs, pQuant calculates the relative heavy/light peptide ratios along with their 99.75% confidence intervals (CIs). From the peptides ratios and their CIs, pQuant estimates the protein ratios and associated CIs by kernel density estimation. We tested pQuant, Census and MaxQuant on data sets obtained from mixtures (at varying mixing ratios from 10:1 to 1:10) of light- and heavy-SILAC labeled HeLa cells or ¹⁴N- and ¹⁵N-labeled Escherichia coli cells. pQuant quantitated more peptides with better accuracy than Census and MaxQuant in all 14 data sets. On the SILAC data sets, the nonquantified 鈥淣aN鈥?(not a number) ratios generated by Census, MaxQuant, and pQuant accounted for 2.5鈥?0.7%, 1.8鈥?.7%, and 0.01鈥?.5% of all ratios, respectively. On the ¹⁴N/¹⁵N data sets, which cannot be quantified by MaxQuant, Census and pQuant produced 0.9鈥?0.0% and 0.3鈭?.9% NaN ratios, respectively. Excluding these NaN results, the standard deviations of the numerical ratios calculated by Census or MaxQuant are 30鈥?00% larger than those by pQuant. These results show that pQuant outperforms Census and MaxQuant in SILAC and ¹⁵N-based quantitation.