mSet: LC/MS data mSet object example

In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

LC/MS data mSet object example

Description

Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)

Usage

data("mSet")

References

Chambers, C. M, Maclean, Brendan, Burke, Robert, Amodei, Dario, Ruderman, L. D, Neumann, Steffen, Gatto, Laurent, Fischer, Bernd, Pratt, Brian, Egertson, Jarrett, Hoff, Katherine, Kessner, Darren, Tasman, Natalie, Shulman, Nicholas, Frewen, Barbara, Baker, A. T, Brusniak, Mi-Youn, Paulse, Christopher, Creasy, David, Flashner, Lisa, Kani, Kian, Moulding, Chris, Seymour, L. S, Nuwaysir, M. L, Lefebvre, Brent, Kuhlmann, Frank, Roark, Joe, Rainer, Paape, Detlev, Suckau, Hemenway, Tina, Huhmer, Andreas, Langridge, James, Connolly, Brian, Chadick, Trey, Holly, Krisztina, Eckels, Josh, Deutsch, W. E, Moritz, L. R, Katz, E. J, Agus, B. D, MacCoss, Michael, Tabb, L. D, Mallick, Parag (2012). “A cross-platform toolkit for mass spectrometry and proteomics.” Nat Biotech, 30(10), 918–920. doi: 10.1038/nbt.2377, http://dx.doi.org/10.1038/nbt.2377.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz P, Deutsch EW (2010). “mzML - a Community Standard for Mass Spectrometry Data.” Mol Cell Proteomics. doi: 10.1074/mcp.R110.000133.

Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (2004). “A common open representation of mass spectrometry data and its application to proteomics research.” Nat Biotechnol, 22(11), 1459–1466. doi: 10.1038/nbt1031.

Keller A, Eng J, Zhang N, Li X, Aebersold R (2005). “A uniform proteomics MS/MS analysis platform utilizing open XML file formats.” Mol Syst Biol.

Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008). “ProteoWizard: open source software for rapid proteomics tools development.” Bioinformatics, 24(21), 2534–2536. doi: 10.1093/bioinformatics/btn323.

Examples

data(mSet)
## maybe str(mSet) ; plot(mSet) ...

xia-lab/OptiLCMS documentation built on Nov. 6, 2024, 11:01 a.m.