12 years ago, scientists have declared achievement of the human genome project. Just one year ago, scientists have published the human proteome project. The finish of these two goals is heavily dependent on two technology, DNA sequencing and mass spectrometry. Here, we introduce the newly developed method sequential window acquisition of all theoretical mass spectra (SWATH).
The applications of mass spectrometry to life science increased sharply. The quantitative proteomics uses stable isotopes, or label-free method to measure relative protein abundance. The isotope labeling strategies are more precise and accurate compared to label-free methods, but labeling procedures are complicated and expensive, and the sample number and types are also limited. SWATH is a recently developed methodology, The key of this methods is a large scale MRM with increased throughput by using data-independent acquisition.
Firstly, we use mouse cell lysate to generate a peptide spectral library employed by shotgun. In total 3600 proteins got identified and quantified without sample prefractionation. The comparison between three technical replicates for each sample shows a high quantification precision and accuracy when protein abundance ratios are equal. The SWATH method shows outstanding quantification precision, whereas the quantification accuracy becomes less perfect when protein abundances differ greatly.
To summary, this study shows the SWATH quantitative method is able to quantify protein abundance precisely, and more, can provide quantification information on proteome-scale.