Data

Tools

Indexes

Applications

Experiments

Open Source Science

IDSL.NPA

A pipeline for processing nominal mass spectrometry data to create .msp files for untargeted MS/MS workflows.

https://github.com/idslme/idsl.npa

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.9%) to scientific vocabulary

Keywords

cran gcms mass-spectrometry metabolomics r spectral-entropy
Last synced: 8 months ago · JSON representation

Repository

A pipeline for processing nominal mass spectrometry data to create .msp files for untargeted MS/MS workflows.

Basic Info
  • Host: GitHub
  • Owner: idslme
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 1.02 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
cran gcms mass-spectrometry metabolomics r spectral-entropy
Created almost 4 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License

README.md

IDSL.NPA

Developed-by CRAN status Dependencies <!-- badges: end -->

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), 94809487.

Owner

  • Name: Integrated Data Science Laboratory for Metabolomics and Exposomics
  • Login: idslme
  • Kind: organization
  • Location: New York

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 227 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: IDSL.NPA

Nominal Peak Analysis (NPA)

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 227 Last month
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Average: 42.7%
Downloads: 84.1%
Maintainers (1)
dinesh.barupal@mssm.edu
Last synced: 9 months ago

Dependencies

IDSL.NPA/DESCRIPTION cran
  • R >= 4.0 depends
  • IDSL.FSA * imports
  • IDSL.IPA >= 2.6 imports
  • IDSL.MXP >= 1.8 imports
  • doParallel * imports
  • foreach * imports
  • readxl * imports