Ms1 Composite Spectra Deconvolution

MS1-only Composite Spectra deconvolution

Summary

MS1-only Composite Spectra Analysis (CSA) deconvolves fragmentation spectra from precursor mass-to-charge and retention time information alone, without reliance on tandem MS/MS data. This method is implemented in IDSL.CSA to streamline chemical structure annotation in untargeted metabolomics and exposomics workflows.

When to use

Apply this skill when you have high-resolution MS1 data (mzXML, mzML, or netCDF format) from LC/HRMS analysis and need to deconvolve composite spectra into individual fragmentation patterns without DDA or DIA acquisition. Use it particularly for large population studies (n > 500) where you want to improve chemical structure annotation by aggregating annotated structures across aligned peaks using metadata such as InChIKey, SMILES, precursor type, or molecular formula.

When NOT to use

• Input data already includes DDA or DIA fragmentation spectra; use the appropriate DDA or DIA analysis mode in IDSL.CSA instead.
• Raw mass spectrometry data has not been pre-processed by IDSL.IPA; chromatographic m/z-RT information is a mandatory prerequisite.
• Study population size is very small (n < 10) where peak alignment and aggregation across samples may be unreliable.

Inputs

• mzXML, mzML, or netCDF raw mass spectrometry data files
• peaklists directory (output from IDSL.IPA workflow)
• peak_alignment directory (output from IDSL.IPA workflow)
• IDSL.CSA parameter spreadsheet (CSA_parameters.xlsx) with configured parameters

Outputs

• MSP files (deconvoluted fragmentation spectra with annotations)
• adduct_annotation peaklists (with predicted adduct information)
• peak_alignment_subset (aligned peak tables for major ions in each CSA cluster)
• aligned_spectra_table (CSA aggregation results on aligned peak table)
• batch EIC figures (extracted ion chromatograms for DIA and CSA analyses)

How to apply

First, process raw mass spectrometry data using the IDSL.IPA workflow to obtain m/z-RT chromatographic information and generate aligned peaklists and peak_alignment directories. Next, download and configure the IDSL.CSA parameter spreadsheet (CSA_parameters.xlsx), setting PARAM0001 to YES to process only the CSA workflow. Populate required parameters: CSA0005 (path to MS1 HRMS data), CSA0008 (path to peaklists directory), CSA0009 (path to peak_alignment directory), and CSA0011 (output directory). Adjust CSA0004 (number of processing threads) based on computational resources. Execute the IDSL.CSA_workflow() function with the configured spreadsheet, which will perform peak detection, chromatogram deconvolution, and spectrum aggregation to produce MSP files, adduct annotations, and aligned spectra tables with chemical structure information.

Related tools

• IDSL.CSA (R package that implements MS1-only Composite Spectra deconvolution and orchestrates peak detection, chromatogram deconvolution, spectrum aggregation, and chemical structure annotation) — https://github.com/idslme/IDSL.CSA
• IDSL.IPA (Prerequisite workflow that processes raw mass spectrometry data and generates chromatographic m/z-RT information, peaklists, and peak_alignment outputs required as input to IDSL.CSA)
• IDSL.FSA (Downstream integration for annotating MSP files and generating fragmentation libraries from IDSL.CSA output)
• R (Programming environment in which IDSL.CSA package is executed)

Examples

library(IDSL.CSA)
IDSL.CSA_workflow("/path/to/CSA_parameters.xlsx")

Evaluation signals

• Output MSP files contain fragmentation spectra with non-null m/z and intensity values consistent with precursor masses from the input peaklists.
• Adduct_annotation peaklists show predicted adduct types (e.g., [M+H]+, [M+Na]+, [M-H]-) aligned with input m/z values within instrument mass accuracy (typically < 5 ppm for Orbitrap data).
• aligned_spectra_table demonstrates successful aggregation by grouping peaks with identical or near-identical InChIKey, SMILES, or molecular formula across the study population.
• Peak_alignment_subset files contain fewer peaks than the input aligned peak table, confirming that major ions in each CSA cluster have been successfully extracted.
• Batch EIC figures show distinct, resolved chromatographic peaks with expected retention time ranges and m/z accuracy for the analyzed compound set.

Limitations

• Method relies on high-resolution MS1 data; lower-resolution instruments (TOF, QQQ) may not provide sufficient mass accuracy for reliable deconvolution and chemical annotation.
• Performance depends critically on the quality of input m/z-RT information from IDSL.IPA; poor peak detection or misaligned peaks in the prerequisite workflow will propagate errors into CSA output.
• The approach does not generate fragmentation patterns de novo; it deconvolves composites of existing MS1 signals and requires reference libraries or external fragmentation data for chemical structure confirmation.
• Aggregation across multiple precursor types (adducts, isotopologues, in-source fragments) may produce ambiguous chemical annotations if reference metadata is incomplete or conflicts occur.

Evidence

• [abstract] MS1-only Composite Spectra deconvolution Analysis (CSA): "This package can be used for the deconvolution of fragmentation spectra obtained through various analytical methods such as MS1-only Composite Spectra deconvolution Analysis (CSA)"
• [readme] IDSL.IPA prerequisite and parameter spreadsheet: "Prior to processing your mass spectrometry data (mzXML, mzML, netCDF) using the IDSL.CSA workflow, mass spectrometry data should be processed using the IDSL.IPA workflow to acquire chromatographic"
• [readme] Unique spectra aggregation feature: "Aggregating annotated chemical structures on the aligned peak table using meta-variables such as InChIKey, SMILES, precursor type, molecular formula,... depending on the information in the reference"
• [readme] Output format and purpose: "4.1. CSA_MSP includes .msp file 4.2. CSA_adduct_annotation includes peaklists with potential adduct information 4.3. peak_alignment_subset includes subsets of aligned peak tables for the major ions"
• [readme] Large population study capability: "Analyzing population size untargeted studies (n > 500)"
• [intro] Aim and scope of the skill: "The aim of the IDSL.CSA package is to assist in streamlining the data analysis process and improving the overall chemical structure annotation in the fields of metabolomics and exposomics"