mzkitcpp

mass spectrometry utility functions and processing algorithms written in C++, exposed in R package.

This package has a direct connection to maven_core C++ library, and is the preferred library for wrapping maven_core functionality into R. maven_core implements all non-gui functionality associated with the MAVEN GUI (see maven repo for source code)

Installation

Execute the following command in an R console:

remotes::install_github("calico/mzkitcpp", force=TRUE, build_vignettes=TRUE, upgrade="never")

Local Development

The package can be rebuilt locally during development, without needing to recompile every file.

pkg_dir <- "~/workspace/mzkitcpp"

# need this for new functions, changes to function signatures
Rcpp::compileAttributes(pkg_dir)

# local install will deposit lots of ".o" files in the source folder
install.packages(pkg_dir, type="source", repos=NULL)

# remove .o and .so for clean rebuild (if necessary)
# clean_cpp_pkg <- glue::glue("rm -f {pkg_dir}/src/*.o {pkg_dir}/src/mzkitcpp.so")
# system(clean_cpp_pkg)

Version Changelog

• 1.0.0 initial public release
• 1.1.0 rsecprofiler-related functionality
• 1.2.0 hrms qc app functionality
• 1.3.0 maldesi enhancements for scan-specific parameters
• 1.4.0 add combine_formulas() utility method
• 1.5.0 added get_pressure_trace() utility method
• 1.6.0 added predict_isotopic_envelope() utility method

Functions

• DI_encoded_search_params: Encodes DI search parameters into a formatted string.
• DI_file_info: Extracts file information and scan statistics from DI mzML files.
• DI_ms1_and_ms2_intensity: Extracts MS1 precursor and MS2 fragment intensities for specified m/z values from DI samples.
• DI_ms1_range_intensity: Extracts summed MS1 intensities within specified precursor m/z ranges.
• DI_ms2_range_id: Identifies which MS2 isolation window range each precursor m/z belongs to.
• DI_ms2_ranges: Extracts MS2 isolation window ranges from a DI mzML file.
• DI_ms3_intensity: Extracts MS3 fragment intensities for specified MS1 precursor, MS2 precursor, and MS3 fragment m/z values (typically used for triacylglyceride analysis on ID-X tribrid instruments).
• DI_ms3_peakgroups_and_peaks: Converts MS3 search results to peakgroup and peak table format for database storage.
• DI_ms3_targets: Extracts MS3 target information (MS1 and MS2 precursor m/z pairs) from an mzML file.
• DI_ms_intensity: Extracts intensities for specified m/z values at a given MS level from DI samples.
• DI_peakgroups_and_peaks: Converts DI search results to peakgroup and peak table format for database storage.
• DI_pipeline: Main pipeline for DI MS2 compound identification and quantification.
• DI_pipeline_ms3_search: Pipeline for MS3 analysis, specifying both MS1 and MS2 precursor m/z values (typically for triacylglycerides on ID-X tribrid instruments).
• DI_search_lib: Searches a spectral library against DI MS2 data for compound identification.
• DI_slice_library: Partitions a spectral library by MS2 isolation window ranges for efficient searching.
• DI_summarized_compounds: Summarizes compound identifications using parsimony and fragment evidence.
• DI_unslice_library: Reverses library slicing to restore original library structure.
• ISO_isotope_matrices: Generates isotope distribution matrices for specified compounds.
• adductize_exact_mass: Calculates precursor m/z from an exact mass and adduct.
• adductize_formula: Calculates precursor m/z from a molecular formula and adduct.
• adductize_peptide: Calculates precursor m/z from a peptide sequence and adduct.
• combine_formulas: Combines two columns of molecular formulas in a data frame by merging their elemental compositions (e.g., "C6H12O6" + "H2O" → "C6H14O7"). Returns a data frame with the original columns plus a new combinedFormula column.
• envelope_dist_peptide: Calculates the isotopic envelope distribution for a peptide sequence.
• exact_mass: Calculates the exact (monoisotopic) mass from a molecular formula.
• exact_mass_peptide: Calculates the exact (monoisotopic) mass from a peptide sequence.
• expand_redundant_fragments_ms2_lib: Expands MS2 library entries containing redundant fragments into separate rows.
• expand_redundant_fragments_ms3_lib: Expands MS3 library entries containing redundant fragments into separate rows.
• export_msp_lipids_library: Writes a spectral library DataFrame to an MSP format file.
• findFragPairsGreedyMz: (Deprecated) Matches library and experimental fragment m/z values using greedy algorithm.
• find_duplicate_peaks: Identifies duplicate peaks between original and re-picked peak tables.
• get_background_subtracted_scan_data: Retrieves scan data with background subtraction applied.
• get_consensus_spectrum: Creates a consensus MS2 spectrum from multiple scans within a sample.
• get_eic: Extracts an extracted ion chromatogram (EIC) for a specified m/z and RT range.
• get_last_rts: Retrieves the final retention time from each sample file.
• get_ms2_scans: Extracts MS2 scan information from sample files.
• get_multi_file_consensus_spectrum: Creates a consensus MS2 spectrum from scans across multiple sample files.
• get_pressure_trace: Return pressure trace information from a single mzML file.
• get_scan_data: Retrieves m/z and intensity data for specified scan numbers.
• get_scan_metadata: Retrieves metadata (RT, precursor m/z, MS level, etc.) for specified scans.
• get_standard_rts: Retrieves retention times for internal standards across sample files.
• groups_to_msp_library: Converts peakgroup/peak tables to MSP spectral library format.
• import_msp_lipids_library: Imports an MSP format spectral library into a DataFrame.
• lipidmaps_2020_compound_names: Processes compound names using LipidMaps 2020 nomenclature.
• loop_injections_to_msp_library: Converts loop injection data to MSP spectral library format.
• maldesi_create_modified_mzML: Creates a modified mzML file with adjusted scan parameters for MALDESI data.
• maldesi_decode_params: Decodes MALDESI parameter encodings into structured data frames, supporting both general and compound-specific parameter sets.
• maldesi_isotopic_envelope_finder: Identifies isotopic envelopes in MALDESI imaging mass spectrometry data.
• maldesi_search: Searches for compounds in MALDESI imaging data using exact mass or adduct-based matching.
• mark_fragments_ms2_lib: Marks specific fragments in an MS2 spectral library (e.g., as diagnostic ions).
• match_id_candidates_rcpp: (Deprecated) Matches compound identification candidates based on m/z.
• merge_split_groups: Identifies and merges peakgroups that were incorrectly split during peak detection.
• monoiosotopic_mass: Calculates monoisotopic masses and adducted m/z values for molecular formulas.
• mzk_get_isotope_parameters: Encodes isotope search parameters into a formatted string.
• mzk_get_lipid_parameters: Encodes lipid search parameters into a formatted string.
• name_summaries: Parses and standardizes compound names into structured components.
• peptide_sequence_to_formula: Converts a peptide amino acid sequence to its molecular formula.
• precursor_mass: Calculates precursor m/z values from molecular formulas and adducts.
• predict_formula: Predicts possible molecular formulas from a measured m/z value.
• predict_isotopic_envelope: Computes isotopic envelope natural abundance distribution based on a molecular formula.
• qqq_peaks: Extracts and quantifies peaks from triple quadrupole (QQQ) mass spectrometry data.
• hrms_peaks: Extracts and quantifies peaks from high-resolution liquid chromatography (HRMS) mass spectrometry data.
• record_set_to_msp_library: Converts formatted metabolite records to MSP spectral library format.
• reextract_peaks: Re-extracts peak intensities from raw data using updated parameters.
• repick_peaks: Re-picks peak boundaries and quantifies peaks using updated parameters.
• smoothed_series: Applies smoothing algorithms to time series data.
• update_rts: Updates retention times based on an alignment key.