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. 2009 Jun;8(6):3176-81.
doi: 10.1021/pr800982s.

Accurate and sensitive peptide identification with Mascot Percolator

Markus Brosch  1 , Lu Yu, Tim Hubbard, Jyoti Choudhary
Affiliations

Accurate and sensitive peptide identification with Mascot Percolator

Markus Brosch et al. J Proteome Res. 2009 Jun.

Abstract

Sound scoring methods for sequence database search algorithms such as Mascot and Sequest are essential for sensitive and accurate peptide and protein identifications from proteomic tandem mass spectrometry data. In this paper, we present a software package that interfaces Mascot with Percolator, a well performing machine learning method for rescoring database search results, and demonstrate it to be amenable for both low and high accuracy mass spectrometry data, outperforming all available Mascot scoring schemes as well as providing reliable significance measures. Mascot Percolator can be readily used as a stand alone tool or integrated into existing data analysis pipelines.

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Figures

Figure 1
Figure 1
Illustration of the Mascot Percolator workflow.
Figure 2
Figure 2
For the 20 ppm Mascot search, the basic and extended Mascot Percolator (MP), the Mascot Identity Threshold (MIT) and the Mascot Homology Threshold (MHT) performance were determined as a function of q-value cutoffs ranging from 0 to 0.06. Moreover, the performance of the mass-filtering (5 ppm) strategy, together with the Adjusted Mascot Threshold (AMT) and the emulated Percolator AMT method (MP AMT), is shown for the 500 ppm Mascot search. Note: if no MHT was reported, the MIT was used.
Figure 3
Figure 3
The number of estimated correct PSMs were determined for each q-value cutoff for the basic and extended Mascot Percolator (MP) runs, the Adjusted Mascot Threshold (AMT), the Mascot Identity Threshold (MIT) and Mascot Homology Threshold (MHT) as well as for the Sequest Percolator.
Figure 4
Figure 4
The estimated q-values were plotted against the false discovery rates as reported by the protein standard data set for the extended and the basic Mascot Percolator runs. The dotted lines represent the standard error.
See this image and copyright information in PMC

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