Analogously to the "Lipic_It" function, "Lipic" performs both Type I and Type II corrections in lipid class-related mass spectra. Furthermore, both "Lipic" and "Lipic_It" share the same input and output (see the "Lipic_It" help page for further details). However, the "Lipic" function is not based on a recursive workflow. Hence, the user should refer to it only when reliable dmz values are somehow known.
Lipic(data, z, Res, t = 0.001, span = 25, ppm = 10, xseq = 0.001)
| data | A data frame reporting the recognized sum compositions in the first column. Conversely, the corresponding chemical formulas, the measured m/z, the dmz, and the absolute intensity values need to be listed in the second, third, fourth and fifth columns respectively. N.B. All the elements in the data frame must be sorted following the ascending order of the measured m/z value. Moreover, the "dmz" column must be filled with the corresponding estimates. |
|---|---|
| z | Charge of the lipid ions.The charge sign needs to be specified. |
| Res | Operating resolution of the mass analyzer. |
| t | Probability below which isotope peaks can be omitted. Refer to the "isopattern" function in the "enviPat" package for details. |
| span | The "span" parameter value required by the "pick.peaks" function. This function is included in the "LIPIC" package, but belongs to the "ChemometricsWithR" package. |
| ppm | Accuracy threshold (in ppm) required by the "dmzFind" function. |
| xseq | Increment in the sequence of the m/z values used for the calculation of the simulated mass spectrum employed in dmz calculation. "xseq" is set to 0.001 as default. Higher values reduce the computation time, but can lower the accuracy by which the dmz values are retrieved by the "dmzFind" function. |
A data frame which is an extension of the input data frame. The first five columns are identical to those of the input data frame. The sixth column shows the intensity values after Type II correction. The seventh column shows the intensity values after both Type II and Type I corrections. As indicated by the corresponding headers, the remaining columns show the "Adj" and "Un-Adj" "Lipid Class" percent Relative Abundance and the "Adj" and "Un-Adj" "Most Abundant Lipid" percent Relative Abundance. See the description in the Lipic_It help page for details about the meaning of "Adj" and "Un-Adj".
Andrea Castellaneta, Ilario Losito, Davide Coniglio, Beniamino Leoni, Pietro Santamaria, Maria A. Di Noia, Luigi Palmieri, Cosima D. Calvano, Tommaso R.I. Cataldi: "LIPIC: an automated workflow to account for isotopologues-related interferences in electrospray ionization high resolution mass spectra of phospholipids", Journal of the American Society for Mass Spectrometry, 2021. DOI: https://doi.org/10.1021/jasms.1c00008.
Martin Loos, Christian Gerber, Francesco Corona, Juliane Hollender, Heinz Singer: "Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees" Anal. Chem. 87, 5738–5744 (2015). DOI: https://doi.org/10.1021/acs.analchem.5b00941.
Ron Wehrens: Chemometrics with R. Springer Verlag, Berlin Hei-delberg (2020). DOI: https://doi.org/10.1007/978-3-642-17841-2.
Carson Sievert: "Interactive Web-Based Data Visualization with R, plotly, and shiny" Chapman and Hall/CRC, 2020, https://plotly-r.com.