Msp to csv parsing

msp-to-csv-parsing

Summary

Convert MS/MS spectra from .msp library files into individual CSV library entries with ionisation mode suffixes using the mspToLib function. This skill enables organisation of custom MS/MS fragment libraries for use in metabolite annotation workflows.

When to use

You have a .msp format MS/MS spectrum library (e.g., from MassBank or similar public databases) and need to convert it into individual CSV entries indexed by positive or negative ionisation mode for use as a custom fragment library in MetaboAnnotatoR annotation pipelines.

When NOT to use

• Your spectra are already in individual CSV format or in a pre-built feature library format compatible with MetaboAnnotatoR
• You need to process raw centroid-mode LC-MS AIF chromatograms directly; use xcms + RamClustR preprocessing first
• Your input is already peak-picked pseudo-MS/MS spectra objects from RAMClustR; proceed directly to annotation

Inputs

• .msp file containing MS/MS spectra records (e.g., MassBank_example.msp)
• User-specified output directory path for CSV library entries

Outputs

• Individual CSV library entries (one per spectrum), with filenames tagged with ionisation mode suffix (positive/negative)
• Occurrence scores for peaks above noise and marker peak thresholds

How to apply

Load the .msp file using the mspToLib function from MetaboAnnotatoR, which reads each spectra record and applies default peak-picking parameters: noise threshold of 0.005, marker peaks score of 0.9, and marker peaks threshold of 0.1. These thresholds filter peaks above noise level and assign occurrence scores to peaks meeting the marker peak criteria. The function generates one CSV file per spectrum record, stored in a user-defined output directory, with each filename annotated with a 'positive' or 'negative' ionisation mode suffix based on the spectrum metadata. Verify that all spectrum records from the input .msp file are represented as individual CSV entries with correctly labeled mode suffixes and complete spectral annotations.

Related tools

• MetaboAnnotatoR (Provides mspToLib function for .msp-to-CSV conversion and subsequent metabolite annotation of LC-MS AIF features) — https://github.com/gggraca/MetaboAnnotatoR
• R (Runtime environment (version 4.5.0 or higher) required to execute mspToLib)
• MassBank (Public source of MS/MS spectra in .msp format suitable for conversion into custom libraries)

Examples

mspToLib(mspFile='MassBank_example.msp', outDir='./custom_library', noise=0.005, mpeaksScore=0.9, mpeaksThres=0.1)

Evaluation signals

• All spectra records from the input .msp file are converted to individual CSV files (verify record count matches output file count)
• Each output CSV filename contains an ionisation mode suffix (positive or negative) corresponding to spectrum metadata
• Peak occurrence scores are assigned only to peaks above the noise threshold (0.005) and marker peak threshold (0.1)
• Output CSV structure and column names match the expected MetaboAnnotatoR library format for downstream annotateRC function use
• Spectral annotations are complete with m/z values and relative intensities preserved in the CSV entries

Limitations

• Requires input .msp files to contain properly formatted spectra records with ionisation mode metadata; malformed records may be skipped or cause errors
• Default peak-picking parameters (noise=0.005, mpeaksScore=0.9, mpeaksThres=0.1) are fixed in the function; custom thresholds require function modification
• No changelog or version history is available for the MetaboAnnotatoR package, limiting traceability of updates to mspToLib behavior
• Output quality depends on completeness of metadata in the source .msp file (e.g., missing ionisation mode designation may result in ambiguous naming)

Evidence

• [other] The mspToLib function reads and converts spectra records from .msp files into CSV library entries stored in a user-defined directory, with a 'positive' or 'negative' mode suffix added to each file name to facilitate organisation of custom libraries: "mspToLib function reads and converts spectra records from .msp files into CSV library entries stored in a user-defined directory, with a 'positive' or 'negative' mode suffix added to each file name"
• [other] occurrence scores are attributed to peaks above mpeaksThres threshold and noise level using default parameters (noise=0.005, mpeaksScore=0.9, mpeaksThres=0.1): "occurrence scores are attributed to peaks above mpeaksThres threshold and noise level using default parameters (noise=0.005, mpeaksScore=0.9, mpeaksThres=0.1)"
• [readme] Generation of Metabolite fragment database entry from MS/MS spectra from public databases (in .msp format).: "Generation of Metabolite fragment database entry from MS/MS spectra from public databases (in .msp format)"
• [readme] It requires raw LC-MS AIF chromatograms acquired/transformed in centroid mode.: "It requires raw LC-MS AIF chromatograms acquired/transformed in centroid mode"