An integrated quantification method to increase the precision, robustness, and resolution of protein measurement in human plasma samples

Clinical Proteomics

Paul Kearney²  Stephen W Hunsucker²  Kenneth C Fang²  Douglas Spicer²  JoAnne Mulligan²  Matthew McLean³  Pui-Yee Fong²  Mi-Youn Brusniak¹  Clive Hayward²  Lik Wee Lee²  Xiao-jun Li² 

[1] Current address: Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M4-A830, 98109 Seattle, WA, USA;Integrated Diagnostics, 219 Terry Avenue North, Suite 100, 98109 Seattle, WA, USA;Current address: DuPont Industrial Biosciences, 925 Page Mill Road, Palo, 94304 Alto, CA, USA

关键词: Bioinformatics;    Immunoaffinity depletion;    Mass spectrometry;    Clinical proteomics;    Quantitative proteomics;    Plasma or serum analysis;    Multiple reaction monitoring;   

Others  :  1120416
DOI  :  10.1186/1559-0275-12-3

 received in 2014-10-02, accepted in 2014-12-26,  发布年份 2015

【 摘 要 】

Background

Current quantification methods for mass spectrometry (MS)-based proteomics either do not provide sufficient control of variability or are difficult to implement for routine clinical testing.

Results

We present here an integrated quantification (InteQuan) method that better controls pre-analytical and analytical variability than the popular quantification method using stable isotope-labeled standard peptides (SISQuan). We quantified 16 lung cancer biomarker candidates in human plasma samples in three assessment studies, using immunoaffinity depletion coupled with multiple reaction monitoring (MRM) MS. InteQuan outperformed SISQuan in precision in all three studies and tolerated a two-fold difference in sample loading. The three studies lasted over six months and encountered major changes in experimental settings. Nevertheless, plasma proteins in low ng/ml to low μg/ml concentrations were measured with a median technical coefficient of variation (CV) of 11.9% using InteQuan. The corresponding median CV using SISQuan was 15.3% after linear fitting. Furthermore, InteQuan surpassed SISQuan in measuring biological difference among clinical samples and in distinguishing benign versus cancer plasma samples.

Conclusions

We demonstrated that InteQuan is a simple yet robust quantification method for MS-based quantitative proteomics, especially for applications in biomarker research and in routine clinical testing.

【 授权许可】

   
2015 Li et al.; licensee BioMed Central.

【 图 表 】

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