idslme / IDSL.FSA

Fragmentation Spectra Analysis

IDSL.FSA

Fragmentation Spectra Analysis (FSA) by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.ME) is an R package designed to annotate .msp (mass spectra format) and .mgf (Mascot generic format) files using a combination of mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) criteria followed by intelligent pre-filtering steps for rapid searches. IDSL.FSA also provides a number of modules to convert and manipulate .msp and .mgf files.

Table of Contents

• Features of IDSL.FSA
• Installation
• Workflow
• Quick Batch Example
• Wiki
• Citation

Features of IDSL.FSA

1. Parameter selection through a user-friendly and well-described parameter spreadsheet
2. Analyzing population size untargeted studies (n > 500)
3. Consistency with .msp and .mgf file formats
4. Measuring matching variables including mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME)
5. Spectra annotation regardless of presence of precursor values
6. Spectra annotation using optional criteria including retention time and adduct type
7. Spectra annotation using accurate or nominal mass values
8. Generating batch spectra match figures
9. Parallel processing in Windows and Linux environments

Installation

install.packages("IDSL.FSA")

Note: In some instances, the readxl R package is also required to read the FSA parameter spreadsheet.

install.packages("readxl")

Workflow

IDSL.FSA requires Fragmentation Spectra DataBase (FSDB) objects (.Rdata) to rapidly annotate mass spectrometry data (.msp and .mgf). IDSL.FSA is also able to generate FSDB objects from several reference .msp files even with inconsistent settings. When the reference .msp files or FSDB objects are available, to annotate .msp and .mgf files, download the FSA parameter spreadsheet and select the parameters accordingly and then use this spreadsheet as the input for the IDSL.FSA workflow:

library(IDSL.FSA)
FSA_workflow("Address of the FSA parameter spreadsheet")

Quick Batch Example

Follow these steps for a quick msp annotation of an .msp file

1. Download Kynurenine_Kynurenic_acid.msp. You should also ensure this file ends up with an .msp extension after downloading. You may also need to rename this file to have an .msp extension.

2. Download the positive mode FSDB

3. IDSL.FSA requires parameters for three tabs for a full scale run. For this study, use default parameter values presented in the FSA parameter spreadsheet. Then, provide information for

   3.1. FSA0002 for the Address of the MS/MS library (FSDB) generated using FSDB tab

   3.2. FSA0003 for Location of the INPUT sample of .msp and/or .mgf files

   3.3. FSA0004 for Location to save OUTPUT results

   3.4. You may also adjust the number of processing threads using SPEC0001 in the SpectraSimilarity tab according to your computational power

4. Run this command in the R/Rstudio console or terminal.

library(IDSL.FSA)
FSA_workflow("Address of the FSA parameter spreadsheet")

5. You see the results in the address you provided for FSA0004 including:

   5.1. individual SpectraAnnotationTable for each .msp file in the annotated_spectra_tables directory in the .Rdata and .csv formats

   5.2. if you had selected an integer greater than 0 for SPEC0019, match spectra figures are also available in the plot folder for each MSP block.

Wiki

1. Fragmentation Spectra DataBase (FSDB)
2. MSP files management
3. MSP Standardizations
4. Spectral Similarity Metrics

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.