D
Daniel Cociorva
Researcher at Scripps Research Institute
Publications - 20
Citations - 3464
Daniel Cociorva is an academic researcher from Scripps Research Institute. The author has contributed to research in topics: Mass spectrometry & Ion trap. The author has an hindex of 18, co-authored 20 publications receiving 3211 citations. Previous affiliations of Daniel Cociorva include University of Southern California & Federal University of Rio de Janeiro.
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Journal ArticleDOI
Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book
TL;DR: This work reviews the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification.
Journal ArticleDOI
ProLuCID: an improved SEQUEST-like algorithm with enhanced sensitivity and specificity
Tao Xu,Tao Xu,Sung Kyu Park,John D. Venable,James A. Wohlschlegel,Jolene K. Diedrich,Daniel Cociorva,Bingwen Lu,Lujian Liao,J. Hewel,Xuemei Han,Catherine C. L. Wong,Bryan R. Fonslow,Claire M. Delahunty,Yu Gao,H. Shah,John R. Yates +16 more
TL;DR: ProLuCID was able to identify as many as 25% more proteins than SEQUEST and is able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data.
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The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions
Paul C. Denny,Fred K. Hagen,Markus Hardt,Lujian Liao,Weihong Yan,Martha Arellanno,Sara Bassilian,Gurrinder S. Bedi,Pinmannee Boontheung,Daniel Cociorva,Claire M. Delahunty,Trish Denny,Jason Dunsmore,Kym F. Faull,Joyce Gilligan,Mireya Gonzalez-Begne,Frédéric Halgand,Steven C. Hall,Xuemei Han,Bradley S. Henson,Johannes Hewel,Shen Hu,Sherry Jeffrey,Jiang Jiang,Joseph A. Loo,Rachel R. Ogorzalek Loo,Daniel Malamud,James E. Melvin,Olga Miroshnychenko,Mahvash Navazesh,Richard K. Niles,Sung Kyu Park,Akraporn Prakobphol,Prasanna Ramachandran,Megan Richert,Sarah Robinson,Melissa Sondej,Puneet Souda,Mark A. Sullivan,Jona Takashima,Shawn Than,Jianghua Wang,Julian P. Whitelegge,H. Ewa Witkowska,Lawrence E. Wolinsky,Yongming Xie,Tao Xu,Weixia Yu,Jimmy Ytterberg,David T.W. Wong,John R. Yates,Susan J. Fisher +51 more
TL;DR: A catalogue of the salivary proteome of healthy individuals allows future analyses ofSaliva samples from individuals with oral and systemic diseases, with the goal of identifying biomarkers with diagnostic and/or prognostic value for these conditions; another possibility is the discovery of therapeutic targets.
Journal ArticleDOI
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,David L. Tabb,Rovshan G. Sadygov,Michael J. MacCoss,John D. Venable,Johannes Graumann,Jeffrey R. Johnson,Daniel Cociorva,John R. Yates +9 more
TL;DR: A series of unified text file formats for storing spectral data and search results that are compact, easily parsed by both machine and humans, and yet flexible enough to be coupled with new algorithms and data-mining strategies are reported.
Journal ArticleDOI
A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
Alexander W. Bell,Eric W. Deutsch,Catherine E. Au,Robert E. Kearney,Ron Beavis,Salvatore Sechi,Tommy Nilsson,John J.M. Bergeron,Thomas A. Beardslee,Thomas Chappell,Gavin Meredith,Peter J. Sheffield,Phillip Gray,Mahbod Hajivandi,Marshall Pope,Paul F. Predki,Majlinda Kullolli,Marina Hincapie,William S. Hancock,Wei Jia,Lina Song,Lei Li,Junying Wei,Bing Yang,Jinglan Wang,Wantao Ying,Yangjun Zhang,Yun Cai,Xiaohong Qian,Fuchu He,Helmut E. Meyer,Christian Stephan,Martin Eisenacher,Katrin Marcus,Elmar Langenfeld,Caroline May,Steve A. Carr,Rushdy Ahmad,Wenhong Zhu,Jeffrey W. Smith,Samir M. Hanash,Jason J. Struthers,Hong Wang,Qing Zhang,Yanming An,Radoslav Goldman,Elisabet Carlsohn,Sjoerd van der Post,Kenneth E. Hung,David A. Sarracino,Kenneth C. Parker,Bryan Krastins,Raju Kucherlapati,Sylvie Bourassa,Guy G. Poirier,Eugene A. Kapp,Heather Patsiouras,Robert L. Moritz,Richard J. Simpson,Benoit Houle,Sylvie Laboissiere,Pavel Metalnikov,Vivian Nguyen,Tony Pawson,Catherine C. L. Wong,Daniel Cociorva,John R. Yates,Michael J. Ellison,Ana Lopez-Campistrous,P. D. Semchuk,Yueju Wang,Peipei Ping,Giuliano Elia,Michael J. Dunn,Kieran Wynne,Angela K. Walker,John R. Strahler,Philip C. Andrews,Brian L. Hood,William L. Bigbee,Thomas P. Conrads,Derek Smith,Christoph H. Borchers,Gilles A. Lajoie,Sean C. Bendall,Kaye D. Speicher,David W. Speicher,Masanori Fujimoto,Kazuyuki Nakamura,Young Ki Paik,Sang Yun Cho,Min-Seok Kwon,Hyoung Joo Lee,Seul Ki Jeong,An Sung Chung,Christine A. Miller,Rudolf Grimm,Katy Williams,Craig A. Dorschel,Jayson A. Falkner,Lennart Martens,Juan Antonio Vizcaíno +101 more
TL;DR: Central analysis determined missed identifications, environmental contamination, database matching and curation of protein identifications as sources of problems in liquid chromatography–mass spectrometry–based proteomics.