PEAKS - A Software Tool for Shotgun Label Free Proteomics with High Sensitivity and High Accuracy

Figure 5. Summary of Protein Quantification Figure 4. PEAKS Quantified Proteins with High Accuracy and High Sensitivity. (a) Boxplot of the Log Ratios of UPS1 Proteins (b) The Count of Quantified Proteins Overview Label free shotgun proteomics has been used for protein identification and quantification, which are the two most fundamental applications in proteomics. For system-wide application, the sensitivity and accuracy are of the challenge in label-free shotgun proteomics due to the broad dynamic range of protein abundance and stochastic identification of peptides between samples. For intensity-based approach, the information for quantification (MS1) and identification (MS2) is measured in a single run. The deconvolution of overlapped peptide features and retention alignment between runs are the key factors for the data analysis, because the overlapped peptide feature clusters cannot be avoided even with today’s high resolution MS instruments and LC separation techniques. Here we present a software tool, PEAKS Q, for accurate label-free quantification with high sensitivity.