xcms - LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
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immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
14.84 score 234 stars 16 dependents 1.4k scripts 5.1k downloadsmzR - parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
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immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometrycurlopensslcpp
12.53 score 44 stars 49 dependents 257 scripts 8.4k downloadsCAMERA - Collection of annotation related methods for mass spectrometry data
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments
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immunooncologymassspectrometrymetabolomics
9.09 score 14 stars 6 dependents 4 scripts 1.3k downloadsRdisop - Decomposition of Isotopic Patterns
In high resolution mass spectrometry (HR-MS), the measured masses can be decomposed into potential element combinations (chemical sum formulas). Where additional mass/intensity information of respective isotopic peaks is available, decomposition can take this information into account to better rank the potential candidate sum formulas. To compare measured mass/intensity information with the theoretical distribution of candidate sum formulas, the latter needs to be calculated. This package implements fast algorithms to address both tasks, the calculation of isotopic distributions for arbitrary sum formulas (assuming a HR-MS resolution of roughly 30,000), and the ranked list of sum formulas fitting an observed peak or isotopic peak set.
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immunooncologymassspectrometrymetabolomicsmass-spectrometrycpp
8.05 score 5 stars 3 dependents 1.7k downloadsfaahKO - Saghatelian et al. (2004) FAAH knockout LC/MS data
Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet.
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experimentdatamassspectrometrydatadatapkg
4.68 score 1 dependents 802 scriptsmsdata - Various Mass Spectrometry raw data example files
Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines.
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experimentdatamassspectrometrydatadatapkg
4.29 score 327 scripts