How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra?

被引:25
作者
Cox, Juergen [1 ]
Hubner, Nina C. [1 ]
Mann, Matthias [1 ]
机构
[1] Max Planck Inst Biochem, Dept Prote & Signal Transduct, D-82152 Martinsried, Germany
关键词
D O I
10.1016/j.jasms.2008.07.024
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Matching peptide tandem mass spectra to their cognate amino acid sequences in databases is a key step in proteomics. It is u sually performed by assigning a score to a spectrum-sequence combination. De novo sequencing or partial de novo sequencing is useful for organisms without sequenced genome or for peptides with unexpected modifications. Here we use a very large, high accuracy proteomic dataset to investigate how much peptide sequence information is present in tandem mass spectra generated in a linear ion trap (LTQ). More than 400,000 identified tandem mass spectra from a single human cancer cell line project were assigned to 26,896 distinct peptide sequences. The average absolute fragment mass accuracy is 0.102 Da. There are on average about four complementary b- and y-ions; both series are equally represented but y ions are 2- to 3-fold more intense up to mass 1000. Half of all spectra contain uninterrupted b- or y-ion series of at least six amino acids and combining b- and y-ion information yields on average seven amino acid sequences. These sequences are almost always unique in the human proteome, even without using any precursor or peptide sequence tag information. Thus, optimal de novo sequencing algorithms should be able to obtain substantial sequence information in at least half of all cases. (J Am Soc Mass Spectrom 2008, 19, 1813-1820) (c) 2008 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry
引用
收藏
页码:1813 / 1820
页数:8
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