Evaluation of Several MS/MS Search Algorithms for Analysis of Spectra Derived from Electron Transfer Dissociation Experiments
ABSTRACT Electron transfer dissociation (ETD) is increasingly becoming popular for high-throughput experiments especially in the identification of the labile post-translational modifications. Most search algorithms that are currently in use for querying MS/MS data against protein databases have been optimized on the basis of matching fragment ions derived from collision induced dissociation of peptides, which are dominated by b and y ions. However, electron transfer dissociation of peptides generates completely different types of fragments: c and z ions. The goal of our study was to test the ability of different search algorithms to handle data from this fragmentation method. We compared four MS/MS search algorithms (OMSSA, Mascot, Spectrum Mill, and X!Tandem) using approximately 170,000 spectra generated from a standard protein mix, as well as from complex proteomic samples which included a large number of phosphopeptides. Our analysis revealed (1) greater differences between algorithms than has been previously reported for CID data, (2) a significant charge state bias resulting in >60-fold difference in the numbers of matched doubly charged peptides, and (3) identification of 70% more peptides by the best performing algorithm than the algorithm identifying the least number of peptides. Our results indicate that the search engines for analyzing ETD derived MS/MS spectra are still in their early days and that multiple search engines could be used to reduce individual biases of algorithms.
- SourceAvailable from: Mustafa A Barbhuiya[Show abstract] [Hide abstract]
ABSTRACT: Gallbladder cancer is an uncommon but lethal malignancy with particularly high incidence in Chile, India, Japan and China. There is a paucity of unbiased large-scale studies investigating molecular basis of gallbladder cancer. To systematically identify differentially regulated proteins in gallbladder cancer, iTRAQ-based quantitative proteomics of gallbladder cancer was carried out using Fourier transform high resolution mass spectrometry. Of the 2,575 proteins identified, proteins upregulated in gallbladder cancer included several lysosomal proteins such as prosaposin, cathepsin Z and cathepsin H. Downregulated proteins included serine protease HTRA1 and transgelin, which have been reported to be downregulated in several other cancers. Novel biomarker candidates including prosaposin and transgelin were validated to be upregulated and downregulated, respectively, in gallbladder cancer using tissue microarrays. Our study provides the first large scale proteomic characterization of gallbladder cancer which will serve as a resource for future discovery of biomarkers for gallbladder cancer.Biochemical and Biophysical Research Communications 04/2014; 446(4). DOI:10.1016/j.bbrc.2014.03.017 · 2.28 Impact Factor
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ABSTRACT: This paper presents an analysis of a LiNbO<sub>3</sub> electro-optic modulator using the finite difference time domain (FDTD) technique, and also a new and efficient multiresolution time-domain technique for fast and accurate modeling of photonic devices. The electromagnetic fields computed by FDTD are coupled to standard electro-optic relations that characterize electo-optic interactions. This novel approach to LiNbO<sub>3</sub> electro-optic modulators using a coupled FDTD technique allows for previously unattainable investigations into device operating bandwidth and data transmission speed. On the other hand, the proposed multiresolution approach presented in this paper solves Maxwell's equations on nonuniform self-adaptive grids, obtained by applying wavelet transforms followed by hard thresholding. The developed technique is employed to simulate a coplanar waveguide CPW, which represents an electro-optic modulator. Different numerical examples are presented showing more than 75% CPU-time reduction, while maintaining the same degree of accuracy of standard FDTD techniques.Microwave Symposium Digest, 2004 IEEE MTT-S International; 07/2004