CIFTER: Automated Charge-State Determination for Peptide Tandem Mass Spectra

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• 作者：Seungjin Na ; Eunok Paek ; Cheolju Lee
• 刊名：Analytical Chemistry
• 出版年：2008
• 出版时间：March 1, 2008
• 年：2008
• 卷：80
• 期：5
• 页码：1520 - 1528
• 全文大小：410K
• 年卷期：v.80,no.5(March 1, 2008)
• ISSN：1520-6882

文摘

Tandem mass spectrometry (MS/MS) has become acommon and useful tool for analyzing complex proteinmixtures. Database search programs are the most popularmeans for peptide identification from MS/MS spectra.However, estimations of charge states of peptide MS/MSspectra obtained from low-resolution mass spectrometershave not been reliable. They require repetitive databasesearches and additional analyses of the search results.We propose here an algorithm designed to reliably differentiate doubly charged spectra from triply chargedones. We conducted a rigorous analysis of various spectralfeatures and their effects. We employed the distinguishingfeatures found in our analysis and developed a classifierfor multiply charged spectra using a machine learningapproach. The test on various data sets showed that ourmethod could be successfully applied independent ofexperimental setup and mass instrument. This algorithmcan be used to prefilter spectra so that only reasonablygood spectra are submitted to database search programs,thereby saving considerable time. The software for MS/MS charge-state determination, which we named "CIFTER",is available at a website http://prix.uos.ac.kr/sifter/cifter.