Nathan G. Dodder
March 2014
OrgMassSpecR has companion packages that contain mass spectral libraries and functions to compile the libraries into PDF reports. Here, “library” refers to an organized collection of mass spectra, not a collection of R packages.
Each spectral library package is capable of generating a PDF report. This is intended as the primary mechanism for viewing a library, and provides a way to share a library independent of R. Pre-generated reports are not included in the packages. A NIST MSP text file can also be generated. This format can be used to import the spectra into the NIST MS Search software as a custom searchable library.
Within the package source, the spectra and metadata are stored in CSV format. The spectra consist of centroid m/z values and intensities. Chemical structures may be stored in PNG format.
The SpecLibExample package contains a set exogenous compounds identified in a sea lion blubber sample and is used here to illustrate the file structure and functionality of spectral library packages.
Each package has its own LibraryReport function that generates the PDFs. The function is similar across packages, but differences exist to accommodate the the specific needs of the library/project. If multiple spectral library packages are loaded, the appropriate
function should be called using packagename::LibraryReport(). Each page of the PDF report is one spectrum and the associated metadata (compound name, etc.), as shown below.
The m/z labels in the mass spectrum refer to the most abundant peak in the cluster. The peak m/z values listed in the table refer to the monoisotopic peak in the cluster.
The following are notes on creating spectral library packages.
The data directory contains two CSV files. One contains all mass spectra, and the other the metadata for each compound. The help documentation for LibraryReport describes the required column names, which can vary by library package depending on the needs of the project. If used, the directory at /inst/extdata/struct contains PNG files of the chemical structures.
LibraryReport uses the filenames defined in the metadata to select the corresponding spectrum and structure. Therefore, these should be identically specified. The row order within the metadata file controls the page order of the report.
Spectra for the example library were exported from the instrument's data analysis software as NIST MSP text files. Each MSP file was
assigned a unique name. The function OrgMassSpecR::ReadMspDirectory was used to assemble the spectra into a single data frame.
Within LibraryReport, the PNG files at are read and converted to a raster object using png::readPNG. For the example library, the structures were drawn using BKchem, with a font size of 14 and line width of 1 px. They were exported as PNG (Cairo) files at 300 dpi resolution and with a transparent background.