An SILAC quantification algorithm for LC-FTMS

Author

Jian Cui ; Xuepo Ma ; Xiaolin Zhang ; Haskins, W. ; Jiangiu Zhang

Author_Institution

Dept. of Electr. & Comput. Eng., Univ. of Texas at San Antonio, San Antonio, TX, USA

fYear

2012

fDate

2-4 Dec. 2012

Firstpage

199

Lastpage

202

Abstract

Stable isotope labeling by amino acids in cell culture (SILAC) [1] plays an important role in protein biomarker discovery based on liquid chromatography-mass spectrometry (LC-MS). Improvement in quantification accuracy in SILAC labeled LC-MS is needed for reliable biomarker discovery which has been plagued by high false-positive rates. In this paper, we consider various factors, such as interference, noise, and instrument suppression, that influence quantification accuracy, based on which we propose an algorithm with improved performance. Testing on samples with predefined heavy-to-light ratios, shows that our algorithm outperforms leading software by a significant margin in both measures of accuracy and precision.

Keywords

biology computing; cellular biophysics; chromatography; mass spectra; molecular biophysics; proteins; LC-FTMS; SILAC quantification algorithm; amino acids; cell culture; instrument suppression; interference; liquid chromatography-mass spectrometry; noise; protein biomarker discovery; quantification accuracy; stable isotope labeling;

fLanguage

English

Publisher

ieee

Conference_Titel

Genomic Signal Processing and Statistics, (GENSIPS), 2012 IEEE International Workshop on

Conference_Location

Washington, DC

ISSN

2150-3001

Print_ISBN

978-1-4673-5234-5

Type

conf

DOI

10.1109/GENSIPS.2012.6507763

Filename

6507763