Publications by authors named "Daniel Cociorva"

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Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods.
Catherine C L Wong, Daniel Cociorva, Christine A Miller, Alexander Schmidt, Craig Monell

J Proteome Res· February 2013

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Search engine processor: Filtering and organizing peptide spectrum matches.
Paulo C Carvalho, Juliana S G Fischer, Tao Xu, Daniel Cociorva, Tiago S Balbuena

Proteomics· April 2012

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Toward objective evaluation of proteomic algorithms.
John R Yates, Sung Kyu Robin Park, Claire M Delahunty, Tao Xu, Jeffrey N Savas, Daniel Cociorva

Nat Methods· April 2012

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Can the false-discovery rate be misleading?
Rodrigo Barboza, Daniel Cociorva, Tao Xu, Valmir C Barbosa, Jonas Perales

Proteomics· October 2011

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XDIA: improving on the label-free data-independent analysis.
Paulo C Carvalho, Xuemei Han, Tao Xu, Daniel Cociorva, Maria da Gloria Carvalho

Bioinformatics· March 2010

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YADA: a tool for taking the most out of high-resolution spectra.
Paulo C Carvalho, Tao Xu, Xuemei Han, Daniel Cociorva, Valmir C Barbosa

Bioinformatics· October 2009

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Comparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures.
Catherine C L Wong, Daniel Cociorva, John D Venable, Tao Xu, John R Yates

J Am Soc Mass Spectrom· August 2009

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Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra.
Paulo C Carvalho, Daniel Cociorva, Catherine C L Wong, Maria da Gloria da C Carvalho, Valmir C Barbosa

Anal Chem· March 2009

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The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions.
Paul Denny, Fred K Hagen, Markus Hardt, Lujian Liao, Weihong Yan, Daniel Cociorva

J Proteome Res· May 2008

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Motif-specific sampling of phosphoproteomes.
Cristian I Ruse, Daniel B McClatchy, Bingwen Lu, Daniel Cociorva, Akira Motoyama

J Proteome Res· May 2008

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Quantitative mass spectrometry identifies insulin signaling targets in C. elegans.
Meng-Qiu Dong, John D Venable, Nora Au, Tao Xu, Sung Kyu Park, Daniel Cociorva

Science· August 2007

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Optimization of mass spectrometry-compatible surfactants for shotgun proteomics.
Emily I Chen, Daniel Cociorva, Jeremy L Norris, John R Yates

J Proteome Res· July 2007

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Validation of tandem mass spectrometry database search results using DTASelect.
Daniel Cociorva, David L Tabb, John R Yates

Curr Protoc Bioinformatics· January 2007

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Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra.
John D Venable, Tao Xu, Daniel Cociorva, John R Yates

Anal Chem· March 2006

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Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway.
Greg T Cantin, John D Venable, Daniel Cociorva, John R Yates

J Proteome Res· January 2006

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Performance of a linear ion trap-Orbitrap hybrid for peptide analysis.
John R Yates, Daniel Cociorva, Lujian Liao, Vlad Zabrouskov

Anal Chem· January 2006

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Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.
Rovshan G Sadygov, Daniel Cociorva, John R Yates

Nat Methods· December 2004

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MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.
W Hayes McDonald, David L Tabb, Rovshan G Sadygov, Michael J MacCoss, John Venable, Daniel Cociorva

Rapid Commun Mass Spectrom· November 2004

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