Literature DB >> 27571551

MetaMass, a tool for meta-analysis of subcellular proteomics data.

Fridtjof Lund-Johansen1,2, Daniel de la Rosa Carrillo1,3, Adi Mehta1,4, Krzysztof Sikorski1,2, Marit Inngjerdingen1, Tomas Kalina5, Kjetil Røysland6, Gustavo Antonio de Souza1, Andrew R M Bradbury7, Quentin Lecrevisse8,9,10,11, Jan Stuchly5.   

Abstract

We report a tool for the analysis of subcellular proteomics data, called MetaMass, based on the use of standardized lists of subcellular markers. We analyzed data from 11 studies using MetaMass, mapping the subcellular location of 5,970 proteins. Our analysis revealed large variations in the performance of subcellular fractionation protocols as well as systematic biases in protein annotation databases. The Excel and R versions of MetaMass should enhance transparency and reproducibility in subcellular proteomics.

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Year:  2016        PMID： 27571551     DOI： 10.1038/nmeth.3967

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


  18 in total

1.  Open source clustering software.

Authors:  M J L de Hoon; S Imoto; J Nolan; S Miyano
Journal:  Bioinformatics       Date:  2004-02-10       Impact factor: 6.937

2.  Differential detergent fractionation of eukaryotic cells.

Authors:  Melinda Ramsby; Gregory Makowski
Journal:  Cold Spring Harb Protoc       Date:  2011-03-01

Review 3.  Multidimensional proteomics for cell biology.

Authors:  Mark Larance; Angus I Lamond
Journal:  Nat Rev Mol Cell Biol       Date:  2015-04-10       Impact factor: 94.444

4.  Comprehensive assessment of proteins regulated by dexamethasone reveals novel effects in primary human peripheral blood mononuclear cells.

Authors:  Andrea Bileck; Dominique Kreutz; Besnik Muqaku; Astrid Slany; Christopher Gerner
Journal:  J Proteome Res       Date:  2014-11-05       Impact factor: 4.466

5.  Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress.

Authors:  Ana Sofia Carvalho; Helena Ribeiro; Paula Voabil; Deborah Penque; Ole N Jensen; Henrik Molina; Rune Matthiesen
Journal:  Mol Cell Proteomics       Date:  2014-08-15       Impact factor: 5.911

6.  Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes.

Authors:  Serah Choi; Rohith Srivas; Katherine Y Fu; Brian L Hood; Banu Dost; Gregory A Gibson; Simon C Watkins; Bennett Van Houten; Nuno Bandeira; Thomas P Conrads; Trey Ideker; Christopher J Bakkenist
Journal:  J Proteome Res       Date:  2012-09-18       Impact factor: 4.466

7.  Proteomic study of the mucin granulae in an intestinal goblet cell model.

Authors:  Ana M Rodríguez-Piñeiro; Sjoerd van der Post; Malin E V Johansson; Kristina A Thomsson; Alexey I Nesvizhskii; Gunnar C Hansson
Journal:  J Proteome Res       Date:  2012-02-02       Impact factor: 4.466

8.  A quantitative spatial proteomics analysis of proteome turnover in human cells.

Authors:  François-Michel Boisvert; Yasmeen Ahmad; Marek Gierliński; Fabien Charrière; Douglas Lamont; Michelle Scott; Geoff Barton; Angus I Lamond
Journal:  Mol Cell Proteomics       Date:  2011-09-21       Impact factor: 5.911

9.  Impact of missing data imputation methods on gene expression clustering and classification.

Authors:  Marcilio C P de Souto; Pablo A Jaskowiak; Ivan G Costa
Journal:  BMC Bioinformatics       Date:  2015-02-26       Impact factor: 3.169

10.  A draft map of the mouse pluripotent stem cell spatial proteome.

Authors:  Andy Christoforou; Claire M Mulvey; Lisa M Breckels; Aikaterini Geladaki; Tracey Hurrell; Penelope C Hayward; Thomas Naake; Laurent Gatto; Rosa Viner; Alfonso Martinez Arias; Kathryn S Lilley
Journal:  Nat Commun       Date:  2016-01-12       Impact factor: 14.919
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  14 in total

1.  Spatiotemporal Multi-Omics-Derived Atlas of Calcific Aortic Valve Disease.

Authors:  Aldrin V Gomes
Journal:  Circulation       Date:  2018-07-24       Impact factor: 29.690

2.  Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

Authors:  Claire M Mulvey; Lisa M Breckels; Aikaterini Geladaki; Nina Kočevar Britovšek; Daniel J H Nightingale; Andy Christoforou; Mohamed Elzek; Michael J Deery; Laurent Gatto; Kathryn S Lilley
Journal:  Nat Protoc       Date:  2017-05-04       Impact factor: 13.491

3.  Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population.

Authors:  Evan G Williams; Yibo Wu; Witold Wolski; Jun Yong Kim; Jiayi Lan; Moaraj Hasan; Christian Halter; Pooja Jha; Dongryeol Ryu; Johan Auwerx; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2018-06-26       Impact factor: 5.911

4.  Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics.

Authors:  Abla Tannous; Marielle Boonen; Haiyan Zheng; Caifeng Zhao; Colin J Germain; Dirk F Moore; David E Sleat; Michel Jadot; Peter Lobel
Journal:  J Proteome Res       Date:  2020-03-05       Impact factor: 4.466

Review 5.  SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.

Authors:  Taner Arslan; Yanbo Pan; Georgios Mermelekas; Mattias Vesterlund; Lukas M Orre; Janne Lehtiö
Journal:  Nat Protoc       Date:  2022-06-22       Impact factor: 17.021

6.  PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1.

Authors:  Fang Huang; Xia Tang; Bo Ye; Songfeng Wu; Keyue Ding
Journal:  Database (Oxford)       Date:  2022-02-04       Impact factor: 4.462

Review 7.  A Golden Age for Working with Public Proteomics Data.

Authors:  Lennart Martens; Juan Antonio Vizcaíno
Journal:  Trends Biochem Sci       Date:  2017-01-22       Impact factor: 13.807

8.  Correlation profiling of brain sub-cellular proteomes reveals co-assembly of synaptic proteins and subcellular distribution.

Authors:  Nikhil J Pandya; Frank Koopmans; Johan A Slotman; Iryna Paliukhovich; Adriaan B Houtsmuller; August B Smit; Ka Wan Li
Journal:  Sci Rep       Date:  2017-09-21       Impact factor: 4.379

Review 9.  Organellar Maps Through Proteomic Profiling - A Conceptual Guide.

Authors:  Georg H H Borner
Journal:  Mol Cell Proteomics       Date:  2020-04-28       Impact factor: 5.911

10.  High-resolution antibody array analysis of proteins from primary human keratinocytes and leukocytes.

Authors:  Daniel de la Rosa Carrillo; Krzysztof Sikorski; Denis Khnykin; Weiwei Wu; Fridtjof Lund-Johansen
Journal:  PLoS One       Date:  2018-12-27       Impact factor: 3.240
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