IDSL.IPA - Intrinsic Peak Analysis (IPA) for HRMS Data
A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
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exposomefeature-detectionlipidomicsmass-spectrometrymetabolomicspeak-detectionpeak-pickingsmall-moleculeuntargeted-metabolomics
5.53 score 16 stars 4 dependents 35 scripts 206 downloadsIDSL.MXP - Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)
A tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>.
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exposomegc-ms-datalc-ms-datalipidomicsmass-spectrometrymetabolomicsmzmlmzxmlnetcdf
4.57 score 5 stars 5 dependents 1 scripts 382 downloadsIDSL.UFA - United Formula Annotation (UFA) for HRMS Data Processing
A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120> with molecular formulas of a prioritized chemical space using an isotopic profile matching approach. The 'IDSL.UFA' workflow only requires mass spectrometry level 1 (MS1) data for formula annotation. The 'IDSL.UFA' methods was described in <doi:10.1021/acs.analchem.2c00563> .
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exposomeisotopic-distribution-calculationslipidomicsmass-spectrometrymetabolomicsmolecular-formulae-assignmentsmall-molecule
4.08 score 8 stars 1 dependents 10 scripts 176 downloadsIDSL.CSA - Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses
A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.
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composite-spectra-analysiscsadata-dependent-acquisitiondata-independent-acquisitionddadiamass-spectrometrymetabolomicsmetabolomics-pipelinesmall-moleculespectral-entropy
3.78 score 6 stars 20 scripts 189 downloadsIDSL.FSA - Fragmentation Spectra Analysis (FSA)
The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.
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fragmentation-spectramass-spectrometrymassbankmgfmgf-parsermspmsp-parserspectral-entropy
3.48 score 1 stars 2 dependents 173 downloadsIDSL.NPA - Nominal Peak Analysis (NPA)
A pipeline to process nominal mass spectrometry data to create .msp files for untargeted analyses.
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gcmsmass-spectrometrymetabolomicsspectral-entropy
2.70 score 1 stars 183 downloadsIDSL.UFAx - Exhaustive Chemical Enumeration for United Formula Annotation
A pipeline to annotate a number of peaks from the 'IDSL.IPA' peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Si, N, H, As, F, I, Na, O, and P.
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elemental-compositionexposomeisotopic-distribution-calculationslipidomicsmass-spectrometrymetabolomicsmolecular-formulae-assignment
2.70 score 1 stars 3 scripts 142 downloadsIDSL.SUFA - Simplified UFA
A simplified version of the 'IDSL.UFA' package to calculate isotopic profiles and adduct formulas from molecular formulas with no dependency on other R packages for online tools and educational mass spectrometry courses. The 'IDSL.SUFA' package also provides an ancillary module to process user-defined adduct formulas.
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adduct-formulaisotopic-distribution-calculations
2.70 score 124 downloads
