Literature DB >> 24240322

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Rui M M Branca1, Lukas M Orre1, Henrik J Johansson1, Viktor Granholm2, Mikael Huss3, Åsa Pérez-Bercoff4, Jenny Forshed4, Lukas Käll5, Janne Lehtiö4.   

Abstract

We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.

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Year:  2013        PMID： 24240322     DOI： 10.1038/nmeth.2732

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  31 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

2.  Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects.

Authors:  Benjamin J Cargile; Joel R Sevinsky; Amal S Essader; Jerry P Eu; James L Stephenson
Journal:  Electrophoresis       Date:  2008-07       Impact factor: 3.535

3.  Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome.

Authors:  Jacek R Wiśniewski; Alexandre Zougman; Matthias Mann
Journal:  J Proteome Res       Date:  2009-12       Impact factor: 4.466

4.  The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences.

Authors:  B Bjellqvist; G J Hughes; C Pasquali; N Paquet; F Ravier; J C Sanchez; S Frutiger; D Hochstrasser
Journal:  Electrophoresis       Date:  1993-10       Impact factor: 3.535

5.  Myosin gene mutation correlates with anatomical changes in the human lineage.

Authors:  Hansell H Stedman; Benjamin W Kozyak; Anthony Nelson; Danielle M Thesier; Leonard T Su; David W Low; Charles R Bridges; Joseph B Shrager; Nancy Minugh-Purvis; Marilyn A Mitchell
Journal:  Nature       Date:  2004-03-25       Impact factor: 49.962

6.  Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

Authors:  Markus Brosch; Gary I Saunders; Adam Frankish; Mark O Collins; Lu Yu; James Wright; Ruth Verstraten; David J Adams; Jennifer Harrow; Jyoti S Choudhary; Tim Hubbard
Journal:  Genome Res       Date:  2011-04-01       Impact factor: 9.043

7.  De novo derivation of proteomes from transcriptomes for transcript and protein identification.

Authors:  Vanessa C Evans; Gary Barker; Kate J Heesom; Jun Fan; Conrad Bessant; David A Matthews
Journal:  Nat Methods       Date:  2012-11-11       Impact factor: 28.547

8.  A high-resolution map of human evolutionary constraint using 29 mammals.

Authors:  Kerstin Lindblad-Toh; Manuel Garber; Or Zuk; Michael F Lin; Brian J Parker; Stefan Washietl; Pouya Kheradpour; Jason Ernst; Gregory Jordan; Evan Mauceli; Lucas D Ward; Craig B Lowe; Alisha K Holloway; Michele Clamp; Sante Gnerre; Jessica Alföldi; Kathryn Beal; Jean Chang; Hiram Clawson; James Cuff; Federica Di Palma; Stephen Fitzgerald; Paul Flicek; Mitchell Guttman; Melissa J Hubisz; David B Jaffe; Irwin Jungreis; W James Kent; Dennis Kostka; Marcia Lara; Andre L Martins; Tim Massingham; Ida Moltke; Brian J Raney; Matthew D Rasmussen; Jim Robinson; Alexander Stark; Albert J Vilella; Jiayu Wen; Xiaohui Xie; Michael C Zody; Jen Baldwin; Toby Bloom; Chee Whye Chin; Dave Heiman; Robert Nicol; Chad Nusbaum; Sarah Young; Jane Wilkinson; Kim C Worley; Christie L Kovar; Donna M Muzny; Richard A Gibbs; Andrew Cree; Huyen H Dihn; Gerald Fowler; Shalili Jhangiani; Vandita Joshi; Sandra Lee; Lora R Lewis; Lynne V Nazareth; Geoffrey Okwuonu; Jireh Santibanez; Wesley C Warren; Elaine R Mardis; George M Weinstock; Richard K Wilson; Kim Delehaunty; David Dooling; Catrina Fronik; Lucinda Fulton; Bob Fulton; Tina Graves; Patrick Minx; Erica Sodergren; Ewan Birney; Elliott H Margulies; Javier Herrero; Eric D Green; David Haussler; Adam Siepel; Nick Goldman; Katherine S Pollard; Jakob S Pedersen; Eric S Lander; Manolis Kellis
Journal:  Nature       Date:  2011-10-12       Impact factor: 49.962

9.  The quantitative proteome of a human cell line.

Authors:  Martin Beck; Alexander Schmidt; Johan Malmstroem; Manfred Claassen; Alessandro Ori; Anna Szymborska; Franz Herzog; Oliver Rinner; Jan Ellenberg; Ruedi Aebersold
Journal:  Mol Syst Biol       Date:  2011-11-08       Impact factor: 11.429

10.  Novel peptide identification from tandem mass spectra using ESTs and sequence database compression.

Authors:  Nathan J Edwards
Journal:  Mol Syst Biol       Date:  2007-04-17       Impact factor: 11.429
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  105 in total

1.  A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites.

Authors:  Alexander Koch; Daria Gawron; Sandra Steyaert; Elvis Ndah; Jeroen Crappé; Sarah De Keulenaer; Ellen De Meester; Ming Ma; Ben Shen; Kris Gevaert; Wim Van Criekinge; Petra Van Damme; Gerben Menschaert
Journal:  Proteomics       Date:  2014-10-02       Impact factor: 3.984

2.  Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Authors:  Angelika Schmidt; Francesco Marabita; Narsis A Kiani; Catharina C Gross; Henrik J Johansson; Szabolcs Éliás; Sini Rautio; Matilda Eriksson; Sunjay Jude Fernandes; Gilad Silberberg; Ubaid Ullah; Urvashi Bhatia; Harri Lähdesmäki; Janne Lehtiö; David Gomez-Cabrero; Heinz Wiendl; Riitta Lahesmaa; Jesper Tegnér
Journal:  BMC Biol       Date:  2018-05-07       Impact factor: 7.431

3.  GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.

Authors:  Jia Zhang; Ming-Kun Yang; Honghui Zeng; Feng Ge
Journal:  Mol Cell Proteomics       Date:  2016-09-14       Impact factor: 5.911

4.  Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes.

Authors:  Ming-kun Yang; Yao-hua Yang; Zhuo Chen; Jia Zhang; Yan Lin; Yan Wang; Qian Xiong; Tao Li; Feng Ge; Donald A Bryant; Jin-dong Zhao
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

5.  PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer.

Authors:  Andrä Brunner; Aldwin Suryo Rahmanto; Henrik Johansson; Marcela Franco; Johanna Viiliäinen; Mohiuddin Gazi; Oliver Frings; Erik Fredlund; Charles Spruck; Janne Lehtiö; Juha K Rantala; Lars-Gunnar Larsson; Olle Sangfelt
Journal:  Elife       Date:  2020-07-06       Impact factor: 8.140

6.  Noncanonical open reading frames encode functional proteins essential for cancer cell survival.

Authors:  John R Prensner; Oana M Enache; Victor Luria; Karsten Krug; Karl R Clauser; Joshua M Dempster; Amir Karger; Li Wang; Karolina Stumbraite; Vickie M Wang; Ginevra Botta; Nicholas J Lyons; Amy Goodale; Zohra Kalani; Briana Fritchman; Adam Brown; Douglas Alan; Thomas Green; Xiaoping Yang; Jacob D Jaffe; Jennifer A Roth; Federica Piccioni; Marc W Kirschner; Zhe Ji; David E Root; Todd R Golub
Journal:  Nat Biotechnol       Date:  2021-01-28       Impact factor: 54.908

7.  A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility.

Authors:  Bei Wei; Arttu Jolma; Biswajyoti Sahu; Lukas M Orre; Fan Zhong; Fangjie Zhu; Teemu Kivioja; Inderpreet Sur; Janne Lehtiö; Minna Taipale; Jussi Taipale
Journal:  Nat Biotechnol       Date:  2018-05-21       Impact factor: 54.908

8.  The cellular thermal shift assay for evaluating drug target interactions in cells.

Authors:  Rozbeh Jafari; Helena Almqvist; Hanna Axelsson; Marina Ignatushchenko; Thomas Lundbäck; Pär Nordlund; Daniel Martinez Molina
Journal:  Nat Protoc       Date:  2014-08-07       Impact factor: 13.491

9.  SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Authors:  Yafeng Zhu; Lina Hultin-Rosenberg; Jenny Forshed; Rui M M Branca; Lukas M Orre; Janne Lehtiö
Journal:  Mol Cell Proteomics       Date:  2014-04-01       Impact factor: 5.911

Review 10.  Discovery and characterization of smORF-encoded bioactive polypeptides.

Authors:  Alan Saghatelian; Juan Pablo Couso
Journal:  Nat Chem Biol       Date:  2015-12       Impact factor: 15.040
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