Literature DB >> 28135259

Building ProteomeTools based on a complete synthetic human proteome.

Daniel P Zolg1, Mathias Wilhelm1, Karsten Schnatbaum2, Johannes Zerweck2, Tobias Knaute2, Bernard Delanghe3, Derek J Bailey4, Siegfried Gessulat1,5, Hans-Christian Ehrlich5, Maximilian Weininger1, Peng Yu1, Judith Schlegl6, Karl Kramer1, Tobias Schmidt1, Ulrike Kusebauch7, Eric W Deutsch7, Ruedi Aebersold8,9, Robert L Moritz7, Holger Wenschuh2, Thomas Moehring3, Stephan Aiche5, Andreas Huhmer4, Ulf Reimer2, Bernhard Kuster1,10,11.   

Abstract

We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography-tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at http://www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange.

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Year:  2017        PMID： 28135259      PMCID： PMC5868332          DOI： 10.1038/nmeth.4153

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


  23 in total

Review 1.  Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides.

Authors:  H Wenschuh; R Volkmer-Engert; M Schmidt; M Schulz; J Schneider-Mergener; U Reineke
Journal:  Biopolymers       Date:  2000       Impact factor: 2.505

2.  MSPLIT-DIA: sensitive peptide identification for data-independent acquisition.

Authors:  Jian Wang; Monika Tucholska; James D R Knight; Jean-Philippe Lambert; Stephen Tate; Brett Larsen; Anne-Claude Gingras; Nuno Bandeira
Journal:  Nat Methods       Date:  2015-12       Impact factor: 28.547

3.  Computational prediction of proteotypic peptides for quantitative proteomics.

Authors:  Parag Mallick; Markus Schirle; Sharon S Chen; Mark R Flory; Hookeun Lee; Daniel Martin; Jeffrey Ranish; Brian Raught; Robert Schmitt; Thilo Werner; Bernhard Kuster; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2006-12-31       Impact factor: 54.908

4.  Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents.

Authors:  Oleg V Krokhin
Journal:  Anal Chem       Date:  2006-11-15       Impact factor: 6.986

Review 5.  Machine learning applications in proteomics research: how the past can boost the future.

Authors:  Pieter Kelchtermans; Wout Bittremieux; Kurt De Grave; Sven Degroeve; Jan Ramon; Kris Laukens; Dirk Valkenborg; Harald Barsnes; Lennart Martens
Journal:  Proteomics       Date:  2014-01-21       Impact factor: 3.984

Review 6.  Protein analysis by shotgun/bottom-up proteomics.

Authors:  Yaoyang Zhang; Bryan R Fonslow; Bing Shan; Moon-Chang Baek; John R Yates
Journal:  Chem Rev       Date:  2013-02-26       Impact factor: 60.622

7.  A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics.

Authors:  Harald Marx; Simone Lemeer; Jan Erik Schliep; Lucrece Matheron; Shabaz Mohammed; Jürgen Cox; Matthias Mann; Albert J R Heck; Bernhard Kuster
Journal:  Nat Biotechnol       Date:  2013-05-19       Impact factor: 54.908

8.  Mass-spectrometry-based draft of the human proteome.

Authors:  Mathias Wilhelm; Judith Schlegl; Hannes Hahne; Amin Moghaddas Gholami; Marcus Lieberenz; Mikhail M Savitski; Emanuel Ziegler; Lars Butzmann; Siegfried Gessulat; Harald Marx; Toby Mathieson; Simone Lemeer; Karsten Schnatbaum; Ulf Reimer; Holger Wenschuh; Martin Mollenhauer; Julia Slotta-Huspenina; Joos-Hendrik Boese; Marcus Bantscheff; Anja Gerstmair; Franz Faerber; Bernhard Kuster
Journal:  Nature       Date:  2014-05-29       Impact factor: 49.962

9.  Using iRT, a normalized retention time for more targeted measurement of peptides.

Authors:  Claudia Escher; Lukas Reiter; Brendan MacLean; Reto Ossola; Franz Herzog; John Chilton; Michael J MacCoss; Oliver Rinner
Journal:  Proteomics       Date:  2012-04       Impact factor: 3.984

10.  Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry.

Authors:  Robert T Lawrence; Brian C Searle; Ariadna Llovet; Judit Villén
Journal:  Nat Methods       Date:  2016-03-28       Impact factor: 28.547
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  52 in total

1.  PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.

Authors:  Luis Francisco Hernández Sánchez; Bram Burger; Carlos Horro; Antonio Fabregat; Stefan Johansson; Pål Rasmus Njølstad; Harald Barsnes; Henning Hermjakob; Marc Vaudel
Journal:  Gigascience       Date:  2019-08-01       Impact factor: 6.524

2.  ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides.

Authors:  Daniel Paul Zolg; Mathias Wilhelm; Tobias Schmidt; Guillaume Médard; Johannes Zerweck; Tobias Knaute; Holger Wenschuh; Ulf Reimer; Karsten Schnatbaum; Bernhard Kuster
Journal:  Mol Cell Proteomics       Date:  2018-05-29       Impact factor: 5.911

3.  Picky: a simple online PRM and SRM method designer for targeted proteomics.

Authors:  Henrik Zauber; Marieluise Kirchner; Matthias Selbach
Journal:  Nat Methods       Date:  2018-02-28       Impact factor: 28.547

4.  PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome.

Authors:  Zhiwu An; Linhui Zhai; Wantao Ying; Xiaohong Qian; Fuzhou Gong; Minjia Tan; Yan Fu
Journal:  Mol Cell Proteomics       Date:  2018-11-12       Impact factor: 5.911

5.  Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework.

Authors:  Korrawe Karunratanakul; Hsin-Yao Tang; David W Speicher; Ekapol Chuangsuwanich; Sira Sriswasdi
Journal:  Mol Cell Proteomics       Date:  2019-10-07       Impact factor: 5.911

Review 6.  Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques.

Authors:  Jesse G Meyer; Birgit Schilling
Journal:  Expert Rev Proteomics       Date:  2017-05       Impact factor: 3.940

7.  Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

Authors:  Gilbert S Omenn; Lydie Lane; Emma K Lundberg; Christopher M Overall; Eric W Deutsch
Journal:  J Proteome Res       Date:  2017-10-09       Impact factor: 4.466

8.  Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics.

Authors:  Clement M Potel; Miao-Hsia Lin; Albert J R Heck; Simone Lemeer
Journal:  Nat Methods       Date:  2018-01-29       Impact factor: 28.547

9.  Mining the Human Tissue Proteome for Protein Citrullination.

Authors:  Chien-Yun Lee; Dongxue Wang; Mathias Wilhelm; Daniel P Zolg; Tobias Schmidt; Karsten Schnatbaum; Ulf Reimer; Fredrik Pontén; Mathias Uhlén; Hannes Hahne; Bernhard Kuster
Journal:  Mol Cell Proteomics       Date:  2018-04-02       Impact factor: 5.911

Review 10.  Expanding the Use of Spectral Libraries in Proteomics.

Authors:  Eric W Deutsch; Yasset Perez-Riverol; Robert J Chalkley; Mathias Wilhelm; Stephen Tate; Timo Sachsenberg; Mathias Walzer; Lukas Käll; Bernard Delanghe; Sebastian Böcker; Emma L Schymanski; Paul Wilmes; Viktoria Dorfer; Bernhard Kuster; Pieter-Jan Volders; Nico Jehmlich; Johannes P C Vissers; Dennis W Wolan; Ana Y Wang; Luis Mendoza; Jim Shofstahl; Andrew W Dowsey; Johannes Griss; Reza M Salek; Steffen Neumann; Pierre-Alain Binz; Henry Lam; Juan Antonio Vizcaíno; Nuno Bandeira; Hannes Röst
Journal:  J Proteome Res       Date:  2018-10-11       Impact factor: 4.466
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