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IDSL.NPA

Developed-by CRAN status Dependencies

Nominal Peak Analysis (NPA) by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.ME) is an R package to facilitate processing of nominal mass spectrometry data. IDSL.NPA encapsulates a peak deconvolution workflow that was inspired by the approach taken by IDSL.CSA, while IDSL.NPA is exclusively capable of processing nominal mass data. Notably, IDSL.NPA does not require MS1 pre-processing to identify MS1 peaks. IDSL.NPA is able to create and annotate .msp files which can be employed for subsequent untargeted MS/MS analysis.

Table of Contents

Features of IDSL.NPA

  1. Parameter selection through a user-friendly and well-described parameter spreadsheet
  2. Analyzing population size untargeted studies (n > 500)
  3. Generating batch untargeted aligned extracted ion chromatograms (EIC) figures.
  4. Parallel processing in Windows and Linux environments
  5. Integration with IDSL.FSA workflow to annotate various types of MSP files and generating fragmentation libraries using nominal mass values.

Installation

install.packages("IDSL.NPA")

Note: In case you want to process netCDF/CDF mass spectrometry data, you should also install the RnetCDF package separately using the below command.

install.packages("RNetCDF")

Workflow

You should download the IDSL.NPA parameter spreadsheet and select the parameters accordingly and then use this spreadsheet as the input for the IDSL.NPA workflow:

library(IDSL.NPA)
IDSL.NPA_workflow("Address of the NPA parameter spreadsheet")

Batch Example

Follow these steps for a case study (n=300) ST001154 which has Agilent 6890N data collected in EI positive mode.

  1. Transfer mass spectrometry data with .cdf extension in a separate folder

  2. The Nominal Mass Analysis requires 24 parameters distributed into 4 separate sections for a full scale analysis. For this study, use default parameter values presented in the NPA parameter spreadsheet. Next, provide information for

    2.1. Select YES for PARAM0001 in the Start tab to only process NPA workflow.

    2.2. NPA0004 for Input data location (MS data)

    2.3. NPA0008 for Output location (.msp files and EICs)

    2.4. You may also increase the number of processing threads using NPA0003 according to your computational power

  3. Run this command in R/Rstudio console or terminal:

library(IDSL.NPA)
IDSL.NPA_workflow("Address of the NPA parameter spreadsheet")
  1. You may parse the results at the address you provided for NPA0008.

Wiki

  1. IDSL.NPA example

Citation

[1] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets. Analytical Chemistry, 2023, 95(25), 9480–9487.