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Relative Quan Label-Free

Discovery-based relative quantification is an analytical approach that allows the scientist to determine relative protein abundance changes across a set of samples simultaneously and without the requirement for prior knowledge of the proteins involved.

To understand the functions of individual proteins and their place in complex biological systems, it is often necessary to measure changes in protein abundance relative to changes in the state of the system. These measurements have traditionally been performed using Western blot analyses. More recently, modern proteomics has evolved to include a variety of technologies for the routine quantitative analyses of both known and unknown targets. Discovery-based relative quantification is an analytical approach that allows the scientist to determine relative protein abundance changes across a set of samples simultaneously and without the requirement for prior knowledge of the proteins involved. Here we describe three commonly used techniques for relative quantitation of unknown protein/peptide targets using mass spectrometry:

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Workflow Overview for Label-Free Relative Quantitation


Label-free relative quantitation involves comparing the abundances of proteins in multiple samples without the use of isotopic labels.  Samples are run individually, then common chromatographic features are used to align the various runs with software. Signals corresponding to individual peptide ions are integrated over the LC time scale, and compared between runs. Label-free analysis is a powerful and widely used technique for identifying and quantifying relative changes in complex protein samples. It can be applied to complex biomarker discovery and systems biology studies as well as to isolated proteins and protein complexes. Key benefits of label-free precursor-based quantitation include the fact that unlimited numbers of samples can be compared, samples can be of any origin, and identification of the peptides is not restricted by fragmentation technique, allowing use of CID, ETD, EThcD and/or HCD fragmentation.