title: Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra.
abstract: It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.
authors.affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
authors.forename: Kaijie
authors.initials: K
authors.lastname: Xiao
authors.affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Yu
authors.affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
authors.forename: Houqin
authors.initials: H
authors.lastname: Fang
authors.affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
authors.forename: Bingbing
authors.initials: B
authors.lastname: Xue
authors.affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
authors.forename: Zhixin
authors.initials: Z
authors.lastname: Tian
mesh_terms: D000107:Acetylation; D000465:Algorithms; D000595:Amino Acid Sequence; D002853:Chromatography, Liquid; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D008745:Methylation; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism*; D020543:Proteome / Q000032:analysis*; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry
chemical_list: D029968:Escherichia coli Proteins; D009211:Myoglobin; D020543:Proteome