title: O18Quant: a semiautomatic strategy for quantitative analysis of high-resolution 16O/18O labeled data.
abstract: Proteolytic (18)O-labeling has been widely used in quantitative proteomics since it can uniformly label all peptides from different kinds of proteins. There have been multiple algorithms and tools developed over the last few years to analyze high-resolution proteolytic (16)O/(18)O labeled mass spectra. We have developed a software package, O18Quant, which addresses two major issues in the previously developed algorithms. First, O18Quant uses a robust linear model (RLM) for peptide-to-protein ratio estimation. RLM can minimize the effect of outliers instead of iteratively removing them which is a common practice in other approaches. Second, the existing algorithms lack applicable implementation. We address this by implementing O18Quant using C# under Microsoft.net framework and R. O18Quant automatically calculates the peptide/protein relative ratio and provides a friendly graphical user interface (GUI) which allows the user to manually validate the quantification results at scan, peptide, and protein levels. The intuitive GUI of O18Quant can greatly enhance the user's visualization and understanding of the data analysis. O18Quant can be downloaded for free as part of the software suite ProteomicsTools.
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Masaru
authors.initials: M
authors.lastname: Miyagi
authors.affiliation: Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA ; Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Quanhu
authors.initials: Q
authors.lastname: Sheng
mesh_terms: D000818:Animals; D007553:Isotope Labeling / Q000379:methods; D008297:Male; D013058:Mass Spectrometry / Q000379:methods; D010103:Oxygen Isotopes / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D051381:Rats; D017207:Rats, Sprague-Dawley; D012160:Retina / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D010103:Oxygen Isotopes; D010455:Peptides; D011506:Proteins; D020543:Proteome