Spectrum-based Method to Generate Good Decoy Libraries for Spectral Library Searching in Peptide Identifications

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• 作者：Chia-Ying Cheng ; Chia-Feng Tsai ; Yu-Ju Chen ; Ting-Yi Sung ; Wen-Lian Hsu
• 刊名：Journal of Proteome Research
• 出版年：2013
• 出版时间：May 3, 2013
• 年：2013
• 卷：12
• 期：5
• 页码：2305-2310
• 全文大小：281K
• 年卷期：v.12,no.5(May 3, 2013)
• ISSN：1535-3907

文摘

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the 鈥渟pectrum level鈥?without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

Keywords:

spectral libraries; spectral library searching; target-decoy search; false discovery rate; peptide identification