Probability profiles-novel approach in tandem mass spectrometry De Novo sequencing

Fridman, Tema; Day, Robert M.; Razumovskaya, Jane; Xu, Dong

doi:10.1109/csb.2003.1227351

Cited by 2 publications

(2 citation statements)

References 3 publications

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“…The relevant periodic component in the mass spectrum is due to regularly-spaced peaks corresponding to the monoisotopic species (all 12 C) plus species containing one or more 13 C atoms per ion, with a spacing of ϳ1/z (one u divided by the number of charges on the ion, z); the approximation neglects mass defect and contributions from isotopes of other elements. The spacing of this isotope series can be represented as a sum of delta functions [␦(x) ϭ 1 for x ϭ 0; ϭ 0 for x 0; reference [9], p. 70] spaced at intervals of 1/z and offset from integral multiples of 1/z by the fractional part (⌬ m ) of the actual m/z.…”

Section: Fourier Transform Of a Model For Isotope-resolved Mass Spectramentioning

confidence: 99%

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Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra

Tabb

Shah

Strader

et al. 2006

J. Am. Soc. Mass Spectrom.

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We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from "zoom scan" data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly-through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution. (J Am Soc Mass Spectrom 2006, 17, 903-915)

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Section: Fourier Transform Of a Model For Isotope-resolved Mass Spectramentioning

confidence: 99%

“…The 2 to 3 algorithm [12] uses fragment ion complementarity to discern charge. The PPM-Charger system [13] examines the numbers of putative singlyand doubly-charged fragment ions in the tandem mass spectrum to make this determination. Colinge et al have also developed algorithms to this purpose [14].…”

Section: Charge State Determination For Peptides and Proteinsmentioning

confidence: 99%

Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra

Tabb

Shah

Strader

et al. 2006

J. Am. Soc. Mass Spectrom.

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Genomes to life project : quarterly report October 2003.

Heffelfinger¹

2004

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This SAND report provides the technical progress through October 2003 of the Sandia-led project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling," funded by the DOE Office of Science Genomes to Life Program.Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO 2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO 2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods.This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments.Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus -4 -regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways.The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide everincreasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches...

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Probability profiles-novel approach in tandem mass spectrometry De Novo sequencing

Cited by 2 publications

References 3 publications

Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra

Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra

Genomes to life project : quarterly report October 2003.

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