Introduction
Unanticipated Post-Translational Modifications (PTMs) are common in proteomics. Stephen Tanner et al develop an algorithm " InspecT " to identify PTMs via blind search of mass-spectra ,
which offer a new insight for blind searching [1,2] . You can implement the InspecT" directly at "http://peptide.ucsd.edu/inspect.py" , or download at
"http://peptide.ucsd.edu/ftprepos.html".
But due to the noise in MS/MS data , the complexity of PTMs ,all these identification algorithms can not
avoid high false positive rate and need further validation . So we design kinds of validation methods ( InspecT-Validate ) based on "InspectT", eg : false discover rate (FDR) , princple component analysis .
All these methods are tested based on InspecT using "standard protein mixtures"[3], "standand phosphorylation data" [4] and "blind searching PTMs of histones"(generated by ourselves). Similar approaches can be used to evaluate PTM identifications by other algorithms.
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Reference
- InspecT: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra.
Stephen Tanner, Hongjun Shu, Ari Frank, Ling-Chi Wang, Ebrahim Zandi, Marc Mumby, Pavel A. Pevzner, and Vineet Bafna.
Anal Chem. 2005 Jul 15;77(14):4626-39
- Identification of Post-translational Modifications via Blind Search of Mass-Spectra.
Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner.
Nature Biotechnology 2005 Dec;23(12);1562-7
- Purvine S, Picone AF, Kolker E: Standard mixtures for proteome studies. Omics 2004, 8(1):79-92.
- A probability-based approach for high-throughput protein phosphorylation analysis and site localization.
Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10.
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