Showing 23 of total 23 results (show query)
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 10 days ago.
mass-spectrometrynon-targetcppopenjdk
25.6 match 65 stars 6.22 score 43 scripts
bioc
cliqueMS:Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.
Maintained by Oriol Senan Campos. Last updated 5 months ago.
metabolomicsmassspectrometrynetworknetworkinferencecpp
20.8 match 12 stars 6.91 score 25 scriptsbioc
LOBSTAHS:Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.
Maintained by Henry Holm. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton
20.7 match 8 stars 6.56 score 9 scriptsbioc
MetaboCoreUtils:Core Utils for Metabolomics Data
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.
Maintained by Johannes Rainer. Last updated 5 months ago.
infrastructuremetabolomicsmassspectrometrymass-spectrometry
7.5 match 9 stars 9.40 score 58 scripts 36 dependentsbioc
adductomicsR:Processing of adductomic mass spectral datasets
Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.
Maintained by Josie Hayes. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui
10.8 match 1 stars 4.00 score 5 scripts
idslme
IDSL.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>.
Maintained by Dinesh Barupal. Last updated 2 years ago.
composite-spectra-analysiscsadata-dependent-acquisitiondata-independent-acquisitionddadiamass-spectrometrymetabolomicsmetabolomics-pipelinesmall-moleculespectral-entropy
11.0 match 5 stars 3.40 scorebioc
MAIT:Statistical Analysis of Metabolomic Data
The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.
Maintained by Pol Sola-Santos. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicssoftware
8.0 match 4.60 score 20 scripts
maialba3
LipidMS:Lipid Annotation for LC-MS/MS DDA or DIA Data
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Maintained by M Isabel Alcoriza-Balaguer. Last updated 7 months ago.
6.5 match 2 stars 5.33 score 12 scripts 1 dependents
blosloos
enviPat:Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry
Fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. Loos, M., Gerber, C., Corona, F., Hollender, J., Singer, H. (2015) <doi:10.1021/acs.analchem.5b00941>.
Maintained by Martin Loos. Last updated 8 months ago.
5.0 match 7 stars 6.35 score 48 scripts 7 dependents
taxonomicallyinformedannotation
tima:Taxonomically Informed Metabolite Annotation
This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.
Maintained by Adriano Rutz. Last updated 6 days ago.
metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome
4.5 match 9 stars 6.55 score 32 scripts 2 dependentsidslme
IDSL.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.
Maintained by Dinesh Barupal. Last updated 2 years ago.
adduct-formulaisotopic-distribution-calculations
10.3 match 2.70 scorebioc
metapone:Conducts pathway test of metabolomics data using a weighted permutation test
The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.
Maintained by Tianwei Yu. Last updated 5 months ago.
technologymassspectrometrymetabolomicspathways
6.8 match 4.00 score 9 scriptsbioc
CAMERA: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
Maintained by Steffen Neumann. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
2.5 match 11 stars 10.27 score 175 scripts 6 dependents
janlisec
InterpretMSSpectrum:Interpreting High Resolution Mass Spectra
High resolution mass spectrometry yields often large data sets of spectra from compounds which are not present in available libraries. These spectra need to be annotated and interpreted. 'InterpretMSSpectrum' provides a set of functions to perform such tasks for Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived data in positive and negative ionization mode.
Maintained by Jan Lisec. Last updated 21 days ago.
3.6 match 2 stars 4.56 score 7 scripts 3 dependents
yonghuidong
MSbox:Mass Spectrometry Tools
Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks, examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) ion sources.
Maintained by Yonghui Dong. Last updated 2 years ago.
chemoinformaticsmass-spectrometrymetabolitesmetabolomics
6.1 match 1 stars 2.70 score 10 scriptsbioc
metabCombiner:Method for Combining LC-MS Metabolomics Feature Measurements
This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.
Maintained by Hani Habra. Last updated 5 months ago.
softwaremassspectrometrymetabolomicsmass-spectrometry
2.5 match 10 stars 5.65 score 5 scriptsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
1.7 match 6.19 score 26 scriptsbioc
rgoslin:Lipid Shorthand Name Parsing and Normalization
The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.
Maintained by Nils Hoffmann. Last updated 5 months ago.
softwarelipidomicsmetabolomicspreprocessingnormalizationmassspectrometrycpp
1.5 match 5 stars 5.64 score 22 scriptsidslme
IDSL.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> .
Maintained by Dinesh Barupal. Last updated 2 years ago.
exposomeisotopic-distribution-calculationslipidomicsmass-spectrometrymetabolomicsmolecular-formulae-assignmentsmall-molecule
2.0 match 8 stars 4.08 score 1 scripts 1 dependentsbioc
MassArray:Analytical Tools for MassArray Data
This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.
Maintained by Reid F. Thompson. Last updated 5 months ago.
immunooncologydnamethylationsnpmassspectrometrygeneticsdataimportvisualization
1.9 match 4.30 score 1 scripts
yufree
pmd:Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
Maintained by Miao YU. Last updated 2 months ago.
mass-spectrometrymetabolomicsnon-target
1.1 match 10 stars 6.68 score 40 scriptsrickhelmus
KPIC:Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms
KPIC2 is an effective platform for LC-MS based metabolomics using pure ion chromatograms, which is developed for metabolomics studies. KPIC2 can detect pure ions accurately, align PICs across samples, group PICs to annotate isotope and adduct PICs, fill missing peaks and pattern recognition. High-resolution mass spectrometers like TOF and Orbitrap are more suitable.
Maintained by Hongchao Ji. Last updated 2 years ago.
2.3 match 1.70 score 3 scripts
benbruyneel
massSpectrometryR:massSpectrometryR
Provides calculations, plotting etc for chemistry & mass spectrometry.
Maintained by Ben Bruyneel. Last updated 4 months ago.
mass-spectrometryproteomicsopenjdk
1.7 match 1.70 score 1 scripts