Browsing by Author "Yang, Xu"

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    MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides
    Yang, Xu; Lazar, Iuliana M. (Biomed Central, 2009-03-27)
    Background The discovery of novel protein biomarkers is essential in the clinical setting to enable early disease diagnosis and increase survivability rates. To facilitate differential expression analysis and biomarker discovery, a variety of tandem mass spectrometry (MS/MS)-based protein profiling techniques have been developed. For achieving sensitive detection and accurate quantitation, targeted MS screening approaches, such as multiple reaction monitoring (MRM), have been implemented. Methods MCF-7 breast cancer protein cellular extracts were analyzed by 2D-strong cation exchange (SCX)/reversed phase liquid chromatography (RPLC) separations interfaced to linear ion trap MS detection. MS data were interpreted with the Sequest-based Bioworks software (Thermo Electron). In-house developed Perl-scripts were used to calculate the spectral counts and the representative fragment ions for each peptide. Results In this work, we report on the generation of a library of 9,677 peptides (p < 0.001), representing ~1,572 proteins from human breast cancer cells, that can be used for MRM/MS-based biomarker screening studies. For each protein, the library provides the number and sequence of detectable peptides, the charge state, the spectral count, the molecular weight, the parameters that characterize the quality of the tandem mass spectrum (p-value, DeltaM, Xcorr, DeltaCn, Sp, no. of matching a, b, y ions in the spectrum), the retention time, and the top 10 most intense product ions that correspond to a given peptide. Only proteins identified by at least two spectral counts are listed. The experimental distribution of protein frequencies, as a function of molecular weight, closely matched the theoretical distribution of proteins in the human proteome, as provided in the SwissProt database. The amino acid sequence coverage of the identified proteins ranged from 0.04% to 98.3%. The highest-abundance proteins in the cellular extract had a molecular weight (MW)<50,000. Conclusion Preliminary experiments have demonstrated that putative biomarkers, that are not detectable by conventional data dependent MS acquisition methods in complex un-fractionated samples, can be reliable identified with the information provided in this library. Based on the spectral count, the quality of a tandem mass spectrum and the m/z values for a parent peptide and its most abundant daughter ions, MRM conditions can be selected to enable the detection of target peptides and proteins.
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    Multi-channel Mobile Access to Web Services
    Yang, Xu (Virginia Tech, 2007-11-26)
    To support wireless-oriented services, a new generation of Web services called Mobile services (M-services) has emerged. M-services provide mobile users access to services through wireless networks. One of the important issues in M-service environment is how to discover and access M-services efficiently. In this dissertation, we propose time and power efficient access methods for M-services. We focus on methods for accessing broadcast based M-services from multiple wireless channels. We first discuss efficient access methods in data-oriented wireless broadcast systems. We then discuss how to extend current wireless broadcast systems to support simple M-services. We present a novel infrastructure that provides a multi-channel broadcast framework for mobile users to effectively discover and access composite M-services. Multi-channel algorithms are proposed for efficiently accessing composite services. We define a few semantics that have impact on access efficiency in the proposed infrastructure. We discuss semantic access to composite services. Broadcast channel organizations suitable for discovering and accessing composite services are proposed. We also derive analytical models for these channel organizations. To provide practical study for the proposed infrastructure and access methods, a testbed is developed for simulating accessing M-services in a broadcast-based environment. Extensive experiments have been conducted to study the proposed access methods and broadcast channel organizations. The experimental results are presented and discussed.
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    Quantitative Approaches for Protein Differential Expression Analysis
    Yang, Xu (Virginia Tech, 2009-11-30)
    In this work, tandem mass spectrometry (MS/MS)-based quantitative protocols were developed to facilitate differential protein expression analysis and biomarker discovery via a two-step sample interrogation strategy: (a) global protein profiling and differential expression analysis by spectral counting; and, (b) biomarker candidate validation by targeted screening, i.e., multiple reaction monitoring (MRM). Preliminary experiments were performed to evaluate the performance of the spectral counting method. The method proved to be applicable for proteins with spectral counts≥2, and a close-to-linear relationship between protein concentration and spectral count data was achievable at protein concentration levels <0.1 μM. The detection limit was 40-800 fmol. A protein/peptide library containing ~10,000 peptide entries that facilitates the development of future MRM experiments, was developed. For each protein, the library provides the number and sequence of detectable peptides, the charge state, the spectral count, the molecular weight, the parameters that characterize the quality of the tandem mass spectrum, the peptide retention time, and the top 10 most intense product ions that correspond to a given parent peptide. Only proteins identified by at least two spectral counts are listed. An MRM experiment was performed to demonstrate the successful applicability of this peptide library for the identification of putative biomarkers in proteomic samples.