Stable incorporation of labeled amino acids in cell culture is a simple approach to label proteins in vivo for mass spectrometric quantification. Full incorporation of isotopically heavy amino acids facilitates accurate quantification of proteins from different cultures, yet analysis methods for determination of incorporation are cumbersome and time-consuming. We present QTIPS, Quantification by Total Identified Peptides for SILAC, a straightforward, accurate method to determine the level of heavy amino acid incorporation throughout a population of peptides detected by mass spectrometry. Using QTIPS, we show that the incorporation of heavy amino acids in baker’s yeast is unaffected by the use of prototrophic strains, indicating that auxotrophy is not a requirement for SILAC experiments in this organism. This method has general utility for multiple applications where isotopic labeling is used for quantification in mass spectrometry.

在细胞培养物中稳定掺入标记的氨基酸是一种在体内标记蛋白质以进行质谱定量的简单方法。完全掺入同位素重氨基酸有助于准确定量来自不同培养物的蛋白质，但用于确定掺入的分析方法既麻烦又耗时。我们提出了 QTIPS，通过总识别肽对 SILAC 进行定量，这是一种直接、准确的方法，用于确定通过质谱法检测到的整个肽群中重氨基酸掺入的水平。使用 QTIPS，我们表明面包酵母中重氨基酸的掺入不受使用原养菌株的影响，表明营养缺陷不是该生物体 SILAC 实验的要求。