Literature DB >> 19603827

Reanalysis of Tyrannosaurus rex Mass Spectra.

Marshall Bern1, Brett S Phinney, David Goldberg.   

Abstract

Asara et al. reported the detection of collagen peptides in a 68-million-year-old Tyrannosaurus rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen.

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Year:  2009        PMID： 19603827      PMCID： PMC2738754          DOI： 10.1021/pr900349r

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  13 in total

1.  Qscore: an algorithm for evaluating SEQUEST database search results.

Authors:  Roger E Moore; Mary K Young; Terry D Lee
Journal:  J Am Soc Mass Spectrom       Date:  2002-04       Impact factor: 3.109

2.  Reporting protein identification data: the next generation of guidelines.

Authors:  Ralph A Bradshaw; Alma L Burlingame; Steven Carr; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2006-05       Impact factor: 5.911

3.  Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry.

Authors:  Marshall Bern; Yuhan Cai; David Goldberg
Journal:  Anal Chem       Date:  2007-01-23       Impact factor: 6.986

4.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

Authors:  Joshua E Elias; Steven P Gygi
Journal:  Nat Methods       Date:  2007-03       Impact factor: 28.547

5.  Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.

Authors:  John M Asara; Mary H Schweitzer; Lisa M Freimark; Matthew Phillips; Lewis C Cantley
Journal:  Science       Date:  2007-04-13       Impact factor: 47.728

6.  Interpreting sequences from mastodon and T. rex.

Authors:  John M Asara; John S Garavelli; David A Slatter; Mary H Schweitzer; Lisa M Freimark; Matthew Phillips; Lewis C Cantley
Journal:  Science       Date:  2007-09-07       Impact factor: 47.728

7.  Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores.

Authors:  David Fenyo; Brett S Phinney; Ronald C Beavis
Journal:  J Proteome Res       Date:  2007-03-31       Impact factor: 4.466

8.  Heme compounds in dinosaur trabecular bone.

Authors:  M H Schweitzer; M Marshall; K Carron; D S Bohle; S C Busse; E V Arnold; D Barnard; J R Horner; J R Starkey
Journal:  Proc Natl Acad Sci U S A       Date:  1997-06-10       Impact factor: 11.205

9.  Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".

Authors:  Mike Buckley; Angela Walker; Simon Y W Ho; Yue Yang; Colin Smith; Peter Ashton; Jane Thomas Oates; Enrico Cappellini; Hannah Koon; Kirsty Penkman; Ben Elsworth; Dave Ashford; Caroline Solazzo; Phillip Andrews; John Strahler; Beth Shapiro; Peggy Ostrom; Hasand Gandhi; Webb Miller; Brian Raney; Maria Ines Zylber; M Thomas P Gilbert; Richard V Prigodich; Michael Ryan; Kenneth F Rijsdijk; Anwar Janoo; Matthew J Collins
Journal:  Science       Date:  2008-01-04       Impact factor: 47.728

10.  Molecular phylogenetics of mastodon and Tyrannosaurus rex.

Authors:  Chris L Organ; Mary H Schweitzer; Wenxia Zheng; Lisa M Freimark; Lewis C Cantley; John M Asara
Journal:  Science       Date:  2008-04-25       Impact factor: 47.728
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  22 in total

1.  Target-decoy approach and false discovery rate: when things may go wrong.

Authors:  Nitin Gupta; Nuno Bandeira; Uri Keich; Pavel A Pevzner
Journal:  J Am Soc Mass Spectrom       Date:  2011-05-05       Impact factor: 3.109

2.  Comment on "Unbiased statistical analysis for multi-stage proteomic search strategies".

Authors:  Marshall Bern; Yong J Kil
Journal:  J Proteome Res       Date:  2011-02-21       Impact factor: 4.466

3.  Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen.

Authors:  Ryan C Hill; Matthew J Wither; Travis Nemkov; Alexander Barrett; Angelo D'Alessandro; Monika Dzieciatkowska; Kirk C Hansen
Journal:  Mol Cell Proteomics       Date:  2015-05-06       Impact factor: 5.911

4.  Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities.

Authors:  Evan T Saitta; Renxing Liang; Maggie Cy Lau; Caleb M Brown; Nicholas R Longrich; Thomas G Kaye; Ben J Novak; Steven L Salzberg; Mark A Norell; Geoffrey D Abbott; Marc R Dickinson; Jakob Vinther; Ian D Bull; Richard A Brooker; Peter Martin; Paul Donohoe; Timothy Dj Knowles; Kirsty Eh Penkman; Tullis Onstott
Journal:  Elife       Date:  2019-06-18       Impact factor: 8.140

5.  A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time.

Authors:  Mary H Schweitzer; Wenxia Zheng; Timothy P Cleland; Mark B Goodwin; Elizabeth Boatman; Elizabeth Theil; Matthew A Marcus; Sirine C Fakra
Journal:  Proc Biol Sci       Date:  2013-11-27       Impact factor: 5.349

Review 6.  The fibrillar collagen family.

Authors:  Jean-Yves Exposito; Ulrich Valcourt; Caroline Cluzel; Claire Lethias
Journal:  Int J Mol Sci       Date:  2010-01-28       Impact factor: 6.208

7.  GIP_HUMAN[22-51] is a new proatherogenic peptide identified by native plasma peptidomics.

Authors:  Tsuguto Masaki; Yoshio Kodera; Michishige Terasaki; Kazumi Fujimoto; Tsutomu Hirano; Masayoshi Shichiri
Journal:  Sci Rep       Date:  2021-07-14       Impact factor: 4.379

8.  A molecular phylogeny of Plesiorycteropus reassigns the extinct mammalian order 'Bibymalagasia'.

Authors:  Michael Buckley
Journal:  PLoS One       Date:  2013-03-26       Impact factor: 3.240

9.  Serine protease HtrA1 accumulates in corneal transforming growth factor beta induced protein (TGFBIp) amyloid deposits.

Authors:  Henrik Karring; Ebbe Toftgaard Poulsen; Kasper Runager; Ida B Thøgersen; Gordon K Klintworth; Peter Højrup; Jan J Enghild
Journal:  Mol Vis       Date:  2013-04-12       Impact factor: 2.367

10.  False discovery rates in spectral identification.

Authors:  Kyowon Jeong; Sangtae Kim; Nuno Bandeira
Journal:  BMC Bioinformatics       Date:  2012-11-05       Impact factor: 3.169
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