Abstract of Zhang's talk

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Monday, January 14, 2008

9:30 am – 10:30 am
Conference Room 1206
676 N St. Clair St
Development of peak detection and alignment algorithms for label-free  
quantitative proteomics by LC-MS
Yonghong Zhang, PhD
Windber Research Institute, Windber, PA
Mass spectrometry is widely used in biomedical research for protein  
identification and quantitative analysis. Coupling of HPLC and MS (LC- MS) 
provides a quantitative means for protein analysis with a much  higher 
resolution and through-put than traditional methods such as 2D  gel. 
Quantitative proteomics using LC-MS is a promising method for  biomarker 
discovery and disease profiling. However, the data of LC-MS  analyses can 
not be readily compared because neither features (peaks)  representing 
protein peptides are available, nor features representing  the same protein 
peptide across different samples are matched. Peak  detection and alignment 
play a critical role in quantitative  proteomics using LC-MS and can 
dramatically affect downstream data  analysis. Here we present novel methods 
to detect peptide peaks in LC- MS analyses as a 3D feature (m/z, retention 
time, and intensity)  without data smoothing, and to align peaks across 
different samples by  direct comparison of m/z and retention time matching 
by linear  regression. Performance of the methods is evaluated and compared 
with  methods implemented in MZmine. The result shows that our method is  
more effective and reliable.
Hosts: Warren Kibbe and Simon Lin
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