Literature DB >> 27898063

moFF: a robust and automated approach to extract peptide ion intensities.

Andrea Argentini1,2,3, Ludger J E Goeminne1,2,3,4,5, Kenneth Verheggen1,2,3, Niels Hulstaert1,2,3, An Staes1,2, Lieven Clement3,4, Lennart Martens1,2,3.   

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Year:  2016        PMID： 27898063     DOI： 10.1038/nmeth.4075

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


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  10 in total

1.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Authors:  Jürgen Cox; Matthias Mann
Journal:  Nat Biotechnol       Date:  2008-11-30       Impact factor: 54.908

Review 2.  Peptide and protein quantification: a map of the minefield.

Authors:  Marc Vaudel; Albert Sickmann; Lennart Martens
Journal:  Proteomics       Date:  2010-02       Impact factor: 3.984

3.  SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

Authors:  Marc Vaudel; Harald Barsnes; Frode S Berven; Albert Sickmann; Lennart Martens
Journal:  Proteomics       Date:  2011-01-31       Impact factor: 3.984

4.  PeptideShaker enables reanalysis of MS-derived proteomics data sets.

Authors:  Marc Vaudel; Julia M Burkhart; René P Zahedi; Eystein Oveland; Frode S Berven; Albert Sickmann; Lennart Martens; Harald Barsnes
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

Review 5.  Data processing methods and quality control strategies for label-free LC-MS protein quantification.

Authors:  Marianne Sandin; Johan Teleman; Johan Malmström; Fredrik Levander
Journal:  Biochim Biophys Acta       Date:  2013-04-06

6.  Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches.

Authors:  Ning Qing Liu; Lennard J M Dekker; Christoph Stingl; Coşkun Güzel; Tommaso De Marchi; John W M Martens; John A Foekens; Theo M Luider; Arzu Umar
Journal:  J Proteome Res       Date:  2013-09-13       Impact factor: 4.466

7.  Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

Authors:  Amanda G Paulovich; Dean Billheimer; Amy-Joan L Ham; Lorenzo Vega-Montoto; Paul A Rudnick; David L Tabb; Pei Wang; Ronald K Blackman; David M Bunk; Helene L Cardasis; Karl R Clauser; Christopher R Kinsinger; Birgit Schilling; Tony J Tegeler; Asokan Mulayath Variyath; Mu Wang; Jeffrey R Whiteaker; Lisa J Zimmerman; David Fenyo; Steven A Carr; Susan J Fisher; Bradford W Gibson; Mehdi Mesri; Thomas A Neubert; Fred E Regnier; Henry Rodriguez; Cliff Spiegelman; Stephen E Stein; Paul Tempst; Daniel C Liebler
Journal:  Mol Cell Proteomics       Date:  2009-10-26       Impact factor: 5.911

8.  Asn3, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS.

Authors:  An Staes; Jonathan Vandenbussche; Hans Demol; Marc Goethals; Şule Yilmaz; Niels Hulstaert; Sven Degroeve; Pieter Kelchtermans; Lennart Martens; Kris Gevaert
Journal:  Anal Chem       Date:  2013-11-04       Impact factor: 6.986

9.  ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Authors:  Juan A Vizcaíno; Eric W Deutsch; Rui Wang; Attila Csordas; Florian Reisinger; Daniel Ríos; José A Dianes; Zhi Sun; Terry Farrah; Nuno Bandeira; Pierre-Alain Binz; Ioannis Xenarios; Martin Eisenacher; Gerhard Mayer; Laurent Gatto; Alex Campos; Robert J Chalkley; Hans-Joachim Kraus; Juan Pablo Albar; Salvador Martinez-Bartolomé; Rolf Apweiler; Gilbert S Omenn; Lennart Martens; Andrew R Jones; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2014-03       Impact factor: 54.908

Review 10.  Exploring the potential of public proteomics data.

Authors:  Marc Vaudel; Kenneth Verheggen; Attila Csordas; Helge Raeder; Frode S Berven; Lennart Martens; Juan A Vizcaíno; Harald Barsnes
Journal:  Proteomics       Date:  2015-12-15       Impact factor: 3.984
  10 in total
  24 in total

1.  Ultrafast Peptide Label-Free Quantification with FlashLFQ.

Authors:  Robert J Millikin; Stefan K Solntsev; Michael R Shortreed; Lloyd M Smith
Journal:  J Proteome Res       Date:  2017-11-08       Impact factor: 4.466

2.  Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics.

Authors:  Matthew The; Lukas Käll
Journal:  Mol Cell Proteomics       Date:  2018-11-27       Impact factor: 5.911

3.  Biogeography of microbial bile acid transformations along the murine gut.

Authors:  Solenne Marion; Lyne Desharnais; Nicolas Studer; Yuan Dong; Matheus D Notter; Suresh Poudel; Laure Menin; Andrew Janowczyk; Robert L Hettich; Siegfried Hapfelmeier; Rizlan Bernier-Latmani
Journal:  J Lipid Res       Date:  2020-07-13       Impact factor: 5.922

4.  A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics.

Authors:  Robert J Millikin; Michael R Shortreed; Mark Scalf; Lloyd M Smith
Journal:  J Proteome Res       Date:  2020-04-14       Impact factor: 4.466

5.  Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis.

Authors:  Shichang Liu; Fengchao Yu; Zhu Yang; Tingliang Wang; Hairong Xiong; Caren Chang; Weichuan Yu; Ning Li
Journal:  Mol Cell Proteomics       Date:  2018-02-13       Impact factor: 5.911

6.  The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa.

Authors:  Timothy B Yates; Kai Feng; Jin Zhang; Vasanth Singan; Sara S Jawdy; Priya Ranjan; Paul E Abraham; Kerrie Barry; Anna Lipzen; Chongle Pan; Jeremy Schmutz; Jin-Gui Chen; Gerald A Tuskan; Wellington Muchero
Journal:  Genome Biol Evol       Date:  2021-09-01       Impact factor: 3.416

7.  Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction.

Authors:  Jonathan M Conway; Bennett S McKinley; Nathaniel L Seals; Diana Hernandez; Piyum A Khatibi; Suresh Poudel; Richard J Giannone; Robert L Hettich; Amanda M Williams-Rhaesa; Gina L Lipscomb; Michael W W Adams; Robert M Kelly
Journal:  Appl Environ Microbiol       Date:  2017-12-01       Impact factor: 4.792

8.  Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

Authors:  David J Clark; Saravana M Dhanasekaran; Francesca Petralia; Jianbo Pan; Xiaoyu Song; Yingwei Hu; Felipe da Veiga Leprevost; Boris Reva; Tung-Shing M Lih; Hui-Yin Chang; Weiping Ma; Chen Huang; Christopher J Ricketts; Lijun Chen; Azra Krek; Yize Li; Dmitry Rykunov; Qing Kay Li; Lin S Chen; Umut Ozbek; Suhas Vasaikar; Yige Wu; Seungyeul Yoo; Shrabanti Chowdhury; Matthew A Wyczalkowski; Jiayi Ji; Michael Schnaubelt; Andy Kong; Sunantha Sethuraman; Dmitry M Avtonomov; Minghui Ao; Antonio Colaprico; Song Cao; Kyung-Cho Cho; Selim Kalayci; Shiyong Ma; Wenke Liu; Kelly Ruggles; Anna Calinawan; Zeynep H Gümüş; Daniel Geiszler; Emily Kawaler; Guo Ci Teo; Bo Wen; Yuping Zhang; Sarah Keegan; Kai Li; Feng Chen; Nathan Edwards; Phillip M Pierorazio; Xi Steven Chen; Christian P Pavlovich; A Ari Hakimi; Gabriel Brominski; James J Hsieh; Andrzej Antczak; Tatiana Omelchenko; Jan Lubinski; Maciej Wiznerowicz; W Marston Linehan; Christopher R Kinsinger; Mathangi Thiagarajan; Emily S Boja; Mehdi Mesri; Tara Hiltke; Ana I Robles; Henry Rodriguez; Jiang Qian; David Fenyö; Bing Zhang; Li Ding; Eric Schadt; Arul M Chinnaiyan; Zhen Zhang; Gilbert S Omenn; Marcin Cieslik; Daniel W Chan; Alexey I Nesvizhskii; Pei Wang; Hui Zhang
Journal:  Cell       Date:  2019-10-31       Impact factor: 41.582

9.  Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.

Authors:  Chen Huang; Lijun Chen; Sara R Savage; Rodrigo Vargas Eguez; Yongchao Dou; Yize Li; Felipe da Veiga Leprevost; Eric J Jaehnig; Jonathan T Lei; Bo Wen; Michael Schnaubelt; Karsten Krug; Xiaoyu Song; Marcin Cieślik; Hui-Yin Chang; Matthew A Wyczalkowski; Kai Li; Antonio Colaprico; Qing Kay Li; David J Clark; Yingwei Hu; Liwei Cao; Jianbo Pan; Yuefan Wang; Kyung-Cho Cho; Zhiao Shi; Yuxing Liao; Wen Jiang; Meenakshi Anurag; Jiayi Ji; Seungyeul Yoo; Daniel Cui Zhou; Wen-Wei Liang; Michael Wendl; Pankaj Vats; Steven A Carr; D R Mani; Zhen Zhang; Jiang Qian; Xi S Chen; Alexander R Pico; Pei Wang; Arul M Chinnaiyan; Karen A Ketchum; Christopher R Kinsinger; Ana I Robles; Eunkyung An; Tara Hiltke; Mehdi Mesri; Mathangi Thiagarajan; Alissa M Weaver; Andrew G Sikora; Jan Lubiński; Małgorzata Wierzbicka; Maciej Wiznerowicz; Shankha Satpathy; Michael A Gillette; George Miles; Matthew J Ellis; Gilbert S Omenn; Henry Rodriguez; Emily S Boja; Saravana M Dhanasekaran; Li Ding; Alexey I Nesvizhskii; Adel K El-Naggar; Daniel W Chan; Hui Zhang; Bing Zhang
Journal:  Cancer Cell       Date:  2021-01-07       Impact factor: 31.743

10.  Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets.

Authors:  Suresh Poudel; Alexander L Cope; Kaela B O'Dell; Adam M Guss; Hyeongmin Seo; Cong T Trinh; Robert L Hettich
Journal:  Biotechnol Biofuels       Date:  2021-05-10       Impact factor: 6.040
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