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Fragmentation Spectra Analysis (FSA) by theIntegrated 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.

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

1. Parameter selection through a user-friendly and well-describedparameter 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

install.packages("IDSL.FSA")

Note: In some instances, thereadxl R package is also required to read theFSA parameter spreadsheet.

install.packages("readxl")

IDSL.FSA requiresFragmentation Spectra DataBase (FSDB) objects (.Rdata) to rapidly annotate mass spectrometry data (.msp and.mgf). IDSL.FSA is also able to generateFSDB objects from several reference.msp files even with inconsistent settings. When the reference.msp files orFSDB objects are available, to annotate.msp and.mgf files, download theFSA 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")

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

1. DownloadKynurenine_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 modeFSDB

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

   3.1.FSA0002 for theAddress of the MS/MS library (FSDB) generated usingFSDB tab

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

   3.3.FSA0004 forLocation to save OUTPUT results

   3.4. You may also adjust the number of processing threads usingSPEC0001 in theSpectraSimilarity 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 forFSA0004 including:

   5.1. individualSpectraAnnotationTable for each.msp file in theannotated_spectra_tables directory in the.Rdata and.csv formats

   5.2. if you had selected an integer greater than 0 forSPEC0019, match spectra figures are also available in theplot folder for each MSP block.

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

[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.