Improved label-free LC-MS protein quantification by peptide analysis: A study

In proteomic experiments quantification becomes increasingly important not only for differential proteomic analysis, but also for the identification of specific proteins studying protein complexes (e. g. by affinity purification [1]). Thus, due to increasing sensitivity and scan speed of modern MS instruments, targets and controls show largely overlapping protein patterns with some proteins present in different amounts. In contrast to classical quantification problems, in proteomics samples are highly complex and it is often difficult to decide, which proteins to quantify. An additional problem arises from suppression effects. Fact is, that in complex samples analytes compete for detection [2]. Methods often used in proteomic quantification experiments are e. g. discussed in [3], and the disadvantages of label-based techniques are although mentioned. Thus, labelfree methods will play an important role in the future of proteomic quantification.