PEAKS Benchmarks

PEAKS DB: Database Search

Molecular & Cellular Proteomics published an article written by Zhang et al. regarding PEAKS DB [1]. The paper describes the PEAKS DB search algorithm, which utilizes de novo sequencing to assist database search. This hybrid approach not only significantly increases the accuracy and sensitivity of the database search, but also can report a list of peptides that are found only by de novo sequencing. PEAKS DB was able to find as much as 35% more peptide-spectrum matches than Mascot+Percolator from a standard benchmark data set. The -10lgP score of PEAKS DB, and how it is converted to FDR (false discovery rate), are also introduced in the paper.

PEAKS de novo

Since its initial publication [2], PEAKS' de novo sequencing algorithm has been well-recognized for its accuracy. PEAKS was reported to be the best-performing general de novo sequencing software in multiple third-party publications. Figure 2 shows the result of a comparative study in [3]. In this study PEAKS has the best sensitivity and also has the best performance in the entire range of spectrum quality using the QSTAR data.

ABRF 2012

This year’s ABRF iPRG study “focuses on the evaluation of proteomics laboratories in identifying modified peptides present in a complex mixture.” Researchers were invited to analyze a common LC-MS/MS dataset, and report both the unmodified and modified peptides found in the data. PEAKS achieved outstanding performance in terms of both the total number of correctly identified peptides, and the number of correctly identified modified peptides that were spiked-in the sample (See figure 3). See complete 2012 iPRG Study Results.

ABRF 2011

The iPRG study (via ABRF) allows researchers to benchmark against one another in their ability to accurately identify peptides. The charts found in Figure 4 present a streamlined version of the chart produced by the iPRG study with respect to cases where researchers employed only one peptide identification method in order to give a clear view of independent findings.

Researchers using PEAKS software performed excellently and identified a considerably high quantity of peptides with a very low false discovery rate (FDR). This is just another study illustrating the exceptional capability of PEAKS software in providing a combination of high peptide identification rate and low FDR from database searching. See complete 2011 iPRG Study Results.