ISPTM: an Iterative Search Algorithm for Systematic Identification of Post-translational Modifications from Complex Proteome Mixtures

Authors

Xin Huang, University of Nebraska Medical Center
Lin Huang, University of Nebraska Medical Center
Hong Peng, University of Nebraska Medical Center
Ashu Guru, University of Nebraska - Lincoln
Weihua Zue, University of Nebraska Medical Center
Sang Yong Hong, University of Nebraska Medical Center
Miao Liu, University of Nebraska Medical Center
Seema Sharma, Thermo Fisher Scientific
Kai Fu, University of Nebraska Medical Center
Adam Caprez, University of Nebraska - Lincoln
David Swanson, University of Nebraska-LincolnFollow
Zhixin Zhang, University of Nebraska Medical Center
Shi-Jian Ding, Sanford Burnham Medical Research InstituteFollow

Date of this Version

9-6-2013

Citation

J Proteome Res. 2013 September 6; 12(9): 3831–3842. doi:10.1021/pr4003883.

Abstract

Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in NM associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification than the conventional all-in-one search approach and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures.