Abstract
BackgroundTandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. Traditionally the to-be-measured peptides are fragmented with the collision induced dissociation (CID) method. More recently, the electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. However, the existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID.ResultsTo take full advantage of ETD data, in this paper we develop a new score function to evaluate the match between a peptide and an ETD MS/MS spectrum. Experiments on real data demonstrated that this newly developed score function significantly improved the de novo sequencing accuracy of the PEAKS software on ETD data.ConclusionA new and better score function for ETD MS/MS peptide identification was developed. The method used to develop our ETD score function can be easily reused to train new score functions for other types of MS/MS data.
Highlights
Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics
To better utilize the advantage of electron transfer dissociation (ETD) spectra on longer and more basic peptides, in this paper, we propose a score function for ETD data based on a probabilistic model
We used an ETD dataset of 9885 spectra from a complex C. elegans protein mixture digested with trypsin followed by alkylation with iodoacetamide
Summary
Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. The tobe-measured peptides are fragmented with the collision induced dissociation (CID) method. The electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. The existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID. Tandem mass spectrometry (MS/MS) has become a popular technique in proteomics for protein identification. In a typical “bottom-up” approach, proteins are enzymatically digested into short peptides, each of them is measured with MS/MS and produces an MS/MS spectrum. Many software programs (e.g. Mascot, Sequest and PEAKS) have been developed for MS/MS data analysis [1,2,3,4,5,6].
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