A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

Autor: Michael J. Ellison, Lei Li, John J.M. Bergeron, David W. Speicher, Marina Hincapie, Sjoerd van der Post, Peter J. Sheffield, Catherine C. L. Wong, Thomas A. Beardslee, P. D. Semchuk, Sean C. Bendall, Daniel Cociorva, Wantao Ying, Caroline May, Seul Ki Jeong, Wei Jia, Philip C. Andrews, Steve A. Carr, Benoit Houle, Robert L. Moritz, Lennart Martens, Ana Lopez-Campistrous, Martin Eisenacher, Alexander W. Bell, Raju Kucherlapati, Ron Beavis, Xiaohong Qian, Fuchu He, Brian L. Hood, John R. Yates, Tommy Nilsson, Kieran Wynne, Radoslav Goldman, Vivian Nguyen, Katy Williams, Giuliano Elia, Rudolf Grimm, Salvatore Sechi, Christoph H. Borchers, Yanming An, Masanori Fujimoto, Catherine E. Au, Young Ki Paik, Mahbod Hajivandi, Peipei Ping, Yun Cai, Pavel Metalnikov, Christine A. Miller, Christian Stephan, Wenhong Zhu, Rushdy Ahmad, Marshall Pope, Jinglan Wang, Thomas P. Conrads, Eric W. Deutsch, Min-Seok Kwon, Gilles A. Lajoie, Michael J. Dunn, Guy G. Poirier, Juan Antonio Vizcaíno, William L. Bigbee, Lina Song, John R. Strahler, Sang Yun Cho, Phillip Gray, Craig A. Dorschel, William S. Hancock, Tony Pawson, Kenneth C. Parker, Kaye D. Speicher, Angela K. Walker, Paul F. Predki, Heather Patsiouras, Richard J. Simpson, Thomas Chappell, Kenneth E. Hung, Qing Zhang, Samir M. Hanash, Eugene A. Kapp, Yueju Wang, Katrin Marcus, Jason J. Struthers, Gavin Meredith, Junying Wei, Yangjun Zhang, Sylvie Bourassa, Elisabet Carlsohn, Jayson A. Falkner, Derek Smith, An Sung Chung, Sylvie Laboissiere, Helmut E. Meyer, Hong Wang, Jeffrey W. Smith, Hyoung Joo Lee, David A. Sarracino, Elmar Langenfeld, Kazuyuki Nakamura, Robert E. Kearney, Bing Yang, Bryan Krastins, Majlinda Kullolli

Publikováno v: Nature methods
Biochemistry Publications

We carried out a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in LC-MS-based proteomics. We distributed a test sample consisting of an equimolar mix of 20 highly purified reco

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4b5e903d9691deb1dd901076a5b4974
https://doi.org/10.1038/nmeth.1333

Validated MALDI-TOF/TOF mass spectra for protein standards

Autor: Maureen Kachman, Donna M. Veine, Philip C. Andrews, Angela K. Walker, Jayson A. Falkner, John R. Strahler

Publikováno v: Journal of the American Society for Mass Spectrometry. 18:850-855

A current focus of proteomics research is the establishment of acceptable confidence measures in the assignment of protein identifications in an unknown sample. Development of new algorithmic approaches would greatly benefit from a standard reference

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fc1b37eade29f564057814ee4200ce57
https://doi.org/10.1016/j.jasms.2007.01.010

Rapid Optimization of MRM-MS Instrument Parameters by Subtle Alteration of Precursor and Product m/z Targets

Autor: Jayson A. Falkner, Hamid Mirzaei, Ashley Eastham, Carly A. Sherwood, Lik Wee Lee, Jenni Risler, Daniel Martin

Multiple reaction monitoring (MRM) is a highly sensitive method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides based on the screening of specified precursor peptide-to-fragment ion transitions. MRM-MS

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8e7162046b4b49bf61b863a5a8a0b34d
https://europepmc.org/articles/PMC2811718/

Human Proteinpedia enables sharing of human protein data

Autor: Ron Bose, Jean-Charles Sanchez, Young Jin Lee, Marcus Bantscheff, Pia Hønnerup Jensen, Yunping Zhu, Jonathan C. Trinidad, Juan Martínez-Heredia, Michael Moran, Samir K. Brahmachari, Pierre Gagné, Kripa Shankari, Jeffrey C. Smith, Jose-Manuel Vidal-Taboada, James P. DeLany, Shi Jun Sheng, Ragna Rönnholm, Xosé R. Bustelo, Helene L. Cardasis, Erik Björling, Ole N. Jensen, Pavel Gromov, Michael J. Dunn, Xiaoyue Wang, Guy G. Poirier, Greg T. Cantin, Richard J. Simpson, Kenny Helsens, Ming Zhou, Sumio Sugano, Samir M. Hanash, Prashantha Hebbar, Y. L. Ramachandra, Jennifer E. Van Eyk, Rafael Oliva, Philip C. Andrews, Lennart Martens, Julio E. Celis, B. Abdul Rahiman, Alexander Mehrle, Feixia Chu, Richard D. Smith, Philip A. Cole, Leroi V. DeSouza, Stefan Wiemann, Joseph A. Loo, Bernhard Kuster, Mauno Vihinen, Peter Jung, David C. Muddiman, Jayson A. Falkner, Osamu Ohara, Fredrik Levander, Gerald W. Hart, Mukhtar Ahmed, T. S. Keshava Prasad, Eric W. Deutsch, Riaz Mohmood, Indu Kheterpal, Jeffrey M. Gimble, John R. Yates, Catherine Fenselau, Timothy D. Veenstra, Julian Vasilescu, Brian M. Balgley, Heiko Hermeking, Johanna Salonen, Rainer Pepperkok, Michael Lefevre, William S. Hancock, Visith Thongboonkerd, Tao Xu, Beerelli Seshi, Christine A. Miller, Florian Gnad, Ravi Sirdeshmukh, Arnaud Droit, Renu Goel, Maarit Takatalo, Emanuel F. Petricoin, Mathias Uhlén, Vitor M. Faça, Billy Wu, Robert J. Cotter, Angelo M. De Marzo, Mark E. McComb, Alma S Burlingame, Oliver Hofmann, Martine Morzel, Rajasree Menon, Denis F. Hochstrasser, Peter James, Matthew J. Sullivan, Robin Wait, K. W. Michael Siu, H. C. Harsha, Hainard Alexandre, Megan S. Lim, Winston Hide, Kris Gevaert, Harald Mischak, Thierry Sayd, Matthias Mann, Blagoy Blagoev, Gerard Cagney, Xiangming Fang, Ralph H. Hruban, James D. Morgan, Joel S. Bader, Samuel O. Purvine, Fuchu He, Robert Moritz, Rob M. Ewing, Daniel Figeys, Min-Seok Kwon, Kumaran Kandasamy, Reiko F. Kikuno, Masaaki Oyama, Cecilia Gelfi, Gilbert S. Omenn, James P. McRedmond, Pierre Lescuyer, Kojo S.J. Elenitoba-Johnson, Akhilesh Pandey, Joël Vandekerckhove, Karin Hjernø, Subburaman Mohan, Jens Rick, Kyla Pennington, Raghothama Chaerkady, Henrik Molina, David M Horn, Faith A. Hays, Young Ki Paik, Balamurugan Periaswamy, Giulio Superti-Furga, Roman Körner, Gerard Drewes, Jun Zhong, E. Dransfield, Suresh Mathivanan, Robert H. Rice, David K. Crockett, Thomas A. Neubert, Minna Lehvaslaiho, K. Shivakumar, Catherine E. Costello, Hyoung Joo Lee, Christian Löbke, Keiryn L. Bennett, Nieves Ibarrola, Ramars Amanchy, Petra Zürbig, Vivekananda Shetty, Natalie G. Ahn, Ulrike Korf, J. Daniel Navarro, Anuradha Nalli, Prasanna Ramachandran, David J. States

Publikováno v: Mathivanan, S, Ahmed, M, Ahn, N G, Alexandre, H, Amanchy, R, Andrews, P C, Bader, J S, Balgley, B M, Bantscheff, M, Bennett, K L, Björling, E, Blagoev, B, Bose, R, Brahmachari, S K, Burlingame, A S, Bustelo, X R, Cagney, G, Cantin, G T, Cardasis, H L, Celis, J E, Chaerkady, R, Chu, F, Cole, P A, Costello, C E, Cotter, R J, Crockett, D, DeLany, J P, De Marzo, A M, DeSouza, L V, Deutsch, E W, Dransfield, E, Drewes, G, Droit, A, Dunn, M J, Elenitoba-Johnson, K, Ewing, R M, Van Eyk, J, Faca, V, Falkner, J, Fang, X, Fenselau, C, Figeys, D, Gagné, P, Gelfi, C, Gevaert, K, Gimble, J M, Gnad, F, Goel, R, Gromov, P, Hanash, S M, Hancock, W S, Harsha, H C, Hart, G, Hays, F, He, F, Hebbar, P, Helsens, K, Hermeking, H, Hide, W, Hjernø, K, Hochstrasser, D F, Hofmann, O, Horn, D M, Hruban, R H, Ibarrola, N, James, P, Jensen, O N, Jensen, P H, Jung, P, Kandasamy, K, Kheterpal, I, Kikuno, R F, Korf, U, Körner, R, Kuster, B, Kwon, M-S, Lee, H-J, Lee, Y-J, Lefevre, M, Lehvaslaiho, M, Lescuyer, P, Levander, F, Lim, M S, Löbke, C, Loo, J A, Mann, M, Martens, L, Martinez-Heredia, J, McComb, M, McRedmond, J, Mehrle, A, Menon, R, Miller, C A, Mischak, H, Mohan, S S, Mohmood, R, Molina, H, Moran, M F, Morgan, J D, Moritz, R, Morzel, M, Muddiman, D C, Nalli, A, Navarro, J D, Neubert, T A, Ohara, O, Oliva, R, Omenn, G S, Oyama, M, Paik, Y-K, Pennington, K, Pepperkok, R, Periaswamy, B, Petricoin, E F, Poirier, G G, Prasad, T S K, Purvine, S O, Rahiman, B A, Ramachandran, P, Ramachandra, Y L, Rice, R H, Rick, J, Ronnholm, R H, Salonen, J, Sanchez, J-C, Sayd, T, Seshi, B, Shankari, K, Sheng, S J, Shetty, V, Shivakumar, K, Simpson, R J, Sirdeshmukh, R, Siu, K W M, Smith, J C, Smith, R D, States, D J, Sugano, S, Sullivan, M, Superti-Furga, G, Takatalo, M, Thongboonkerd, V, Trinidad, J C, Uhlen, M, Vandekerckhove, J, Vasilescu, J, Veenstra, T D, Vidal-Taboada, J-M, Vihinen, M, Wait, R, Wang, X, Wiemann, S, Wu, B, Xu, T, Yates, J R, Zhong, J, Zhou, M, Zhu, Y, Zurbig, P & Pandey, A 2008, ' Human Proteinpedia enables sharing of human protein data ', Nature Biotechnology, vol. 26, no. 2, pp. 164-167 . https://doi.org/10.1038/nbt0208-164
Nature Biotechnology
Nature Biotechnology, 2008, 26 (2), pp.164-167. ⟨10.1038/nbt0208-164⟩
Nature Biotechnology, Nature Publishing Group, 2008, 26 (2), pp.164-167. ⟨10.1038/nbt0208-164⟩
Nature Biotechnology, Vol. 26, No 2 (2008) pp. 164-167

Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary inform

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e4d4ec2da9e21964853baaa48a5e228f
https://portal.findresearcher.sdu.dk/da/publications/23073830-00b1-11dd-9e03-000ea68e967b

Open Access to Proteomics Data: A Valuable Resource for Biology and Medicine

Autor: Philip C. Andrews, Jayson A. Falkner

Publikováno v: Journal of Proteome Research. 6:2047-2048

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6852559f0a60c769e2b1aaa001b9f9e2
https://doi.org/10.1021/pr0707509