Package: Aerith 1.0.1

Yi Xiong

Aerith: visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics

Visualisation of peptide isotopic peaks and SIP peptide spectra match (PSM). Filtration of high quality PSM. Accurate isotopic abundance calculation of peptide and metabolites. Visualisation of SIP proteomics results.

Authors:Yi Xiong [aut, cre]

Aerith_1.0.1.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
Aerith/json (API)
NEWS

# Install 'Aerith' in R:
install.packages('Aerith', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/xyz1396/aerith/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:Aerith-1.1.1(bioc 3.24)Aerith-1.0.1(bioc 3.23)

proteomicsmetabolomicsmassspectrometrysoftwarevisualizationqualitycontrolannotationlc-msmass-spectrometrystable-isotope-mass-spectrometrystable-isotope-tracingstable-isotopescppopenmp

6.42 score 5 stars 170 downloads 86 exports 127 dependencies

Last updated from:35fbe1af8e (on RELEASE_3_23). Checks:12 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE251
linux-devel-arm64NOTE315
linux-devel-x86_64NOTE424
source / vignettesOK417
linux-release-arm64NOTE278
linux-release-x86_64NOTE295
macos-release-arm64NOTE251
macos-release-x86_64NOTE669
macos-oldrel-arm64NOTE225
macos-oldrel-x86_64NOTE336
windows-develNOTE285
windows-releaseNOTE240
windows-oldrelNOTE349
wasm-releaseOK221

Exports:annotatePrecursorannotatePSMBYion_peak_calculator_DIYcal_isotope_numberscal_isotope_numbers_SIPcal_isotope_peaks_fftcalBYAtomCountAndBaseMasscalPepAtomCountcalPepNeutronMasscalPepPrecursorMassdenoiseOneMS2ScanHasChargeextractPSMfeaturesextractPSMfeaturesTargetAndDecoyextractPSMfeaturesTargetAndDecoytoPercolatorPingenerateCFGsgenerateOneCFGgetFilterThresholdgetFilterThresholdTopPSMsgetFilterThresholdTopPSMsSpe2PepgetMZgetPrecursorSpectragetRealScangetRealScanFromListgetRealScansgetRealScansWithChargesgetRealScanWithChargegetRetentionTimeAndPrecursorInfogetSipBYionSpectragetSipPrecursorSpectragetTICgetUnfilteredPeptidesgetUnfilteredPSMsplotplotFilteredPCTIntensitySummaryplotMolecularFFTisotopesplotMolecularIsotopesplotPrecursorAnnotationplotPrecursorMzFrequencyplotProSipPctplotPSMannotationplotPSMsplotPSMsipPCTplotRealScanplotScanFrequencyplotScanFrequencyMS2plotScoreDistributionplotSipBYionLabelplotSIPfilteredPCTIntensityBySampleplotTICprecursor_peak_calculatorprecursor_peak_calculator_DIYprecursor_peak_calculator_DIY_averaginerankyfifyreadAllScanMS1readAllScanMS2readFilesScansTopPSMsreadFilesScansTopPSMsFromOneFT2readFTheaderreadMgfreadMzmlMS1readMzmlMS2readOneScanMS1readOneScanMS2readPepXMLtablereadPSMtsvreadScansMS1readScansMS1VectorreadScansMS2readScansMS2VectorreadSipreadSipsreadSpe2PepreadSpe2PepFilesScansTopPSMsreadSpe2PepFilesScansTopPSMsFromEachFT2ParallelreadSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallelreadSpe2PepFilesScansTopPSMsFromOneFT2readSpe2Pepsresidue_peak_calculator_DIYscoreIntensityscoreIntensityByCEscorePSMscorePSMsimplesummaryPSMsipPCTwriteAllScanMS1writeAllScanMS2writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxfunXMLXVectoryaml

Aerith

Rendered fromAerith.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-11-04
Started: 2025-06-14

Input Data Format and File Handling in Aerith

Rendered fromInput-data-format.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-11-12
Started: 2025-03-11

PSM Annotation and Visualization

Rendered fromPSM-annotation-and-visualization.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-23
Started: 2025-02-15

Score function test of PSM

Rendered fromScore-function-test-of-PSM.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-11-04
Started: 2025-03-11

Theoretic spectra generation of SIP-labeled compound

Rendered fromTheoretic-spectra-generation-of-SIP-labeled-compound.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-11-04
Started: 2025-01-09

Theoretic spectra generation of SIP-labeled peptide

Rendered fromTheoretic-spectra-generation-of-SIP-labeled-peptide.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-11-04
Started: 2025-01-09

Visualization of SIP proteomic result

Rendered fromVisualization-of-SIP-proteomic-result.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2025-10-10
Started: 2025-03-11

Readme and manuals

Help Manual

Help pageTopics
AAspectra S4 class for annotated mass spectraAAspectra-class
annotatePrecursorannotatePrecursor
annotatePSMannotatePSM
BY Ion Peak Calculator with User-Defined Isotopic DistributionBYion_peak_calculator_DIY
Calculate Isotope Numbers in natural abundancecal_isotope_numbers
Calculate Isotope Numbers for SIPcal_isotope_numbers_SIP
Calculate Isotope Peaks using FFTcal_isotope_peaks_fft
Simple calculator of C H O N P S atom count and mass without isotope of B Y ionscalBYAtomCountAndBaseMass
Simple calculator of C H O N P S atom count of peptidecalPepAtomCount
Simple calculator neutron mass by average delta mass of each isotopecalPepNeutronMass
Simple calculator of peptide precursor mass by binomial NPcalPepPrecursorMass
denoise one MS2 scan has chargedenoiseOneMS2ScanHasCharge
extractPSMfeatures extract featueres of top PSMs from multiple .Spe2Pep.txt filesextractPSMfeatures
extractPSMfeaturesTargetAndDecoy extract featueres of top PSMs from target and decoy .Spe2Pep.txt filesextractPSMfeaturesTargetAndDecoy
extractPSMfeaturesTargetAndDecoytoPercolatorPin extract featueres of top PSMs from target and decoy .Spe2Pep.txt files to pecorlator pin formatextractPSMfeaturesTargetAndDecoytoPercolatorPin
generateCFGsgenerateCFGs
generateOneCFGgenerateOneCFG
getFilterThresholdgetFilterThreshold
getFilterThresholdTopPSMs get filter threshold of top PSMs of each scan from multiple .sip filegetFilterThresholdTopPSMs
getFilterThresholdTopPSMsSpe2Pep get filter threshold of top PSMs of each scan from multiple .sip filegetFilterThresholdTopPSMsSpe2Pep
add MZ to spectra data.framegetMZ
Get AAspectra object of precursor from AA sequence with natural SIP abundancegetPrecursorSpectra
Convert one scan with charges=1 normalized by highest peak in scans list of ft file to AAspectra classgetRealScan
Convert one scan in list format to AAspectra classgetRealScanFromList
Get real scans from a scans list of one FT file with charges converted to 1 and intensities normalized by the highest peak.getRealScans
get real scans with real charges and raw intensities from scans list of one ft filegetRealScansWithCharges
Convert one scan in scans with real charges and raw intensities from list of scans of ft file to AAspectra classgetRealScanWithCharge
get retention time and precursor mass from scans list of ft filegetRetentionTimeAndPrecursorInfo
Get AAspectra object of B and Y ions from AA sequence with labeled SIP abundancegetSipBYionSpectra
Get AAspectra object of precursor from AA sequence with labeled SIP abundancegetSipPrecursorSpectra
get TIC and retention time from scans list of ft filegetTIC
getUnfilteredPeptidesgetUnfilteredPeptides
getUnfilteredPSMsgetUnfilteredPSMs
Plot an AAspectra objectplot,AAspectra,missing-method plot,AAspectra-method
Plot decoy-filtered PSMs' PCT and intensity summary by each input fileplotFilteredPCTIntensitySummary
Plot Molecular isotopes without fine structure by FFT algorithmplotMolecularFFTisotopes
Plot Molecular Isotopes with fine structure by Montecarlo algorithmplotMolecularIsotopes
plot precursor annotationplotPrecursorAnnotation
Plot precursor MZ frequency per 5 per minute of MS2plotPrecursorMzFrequency
plot the distribution of SIP percent of proteinsplotProSipPct
plot PSM annotationplotPSMannotation
plot PSMs from FT2 files and PSM resultsplotPSMs
Plot the distribution of SIP percent for PSMsplotPSMsipPCT
plot real scan layer under the B Y ion peaksplotRealScan
Plot scan frequencyplotScanFrequency
Plot scan frequency layer of MS2plotScanFrequencyMS2
plot the score of PSMs at different charge and mass errorplotScoreDistribution
Draw AAspectra MS plot with B Y ion LabelsplotSipBYionLabel
Plot SIP-filtered PCT and intensity summary by each input fileplotSIPfilteredPCTIntensityBySample
Plot TIC of MS1 or MS2plotTIC
Precursor Peak Calculatorprecursor_peak_calculator
Precursor Peak Calculator with User-Defined Isotopic Distributionprecursor_peak_calculator_DIY
Simple peak calculator of user defined isotopic distribution of one peptide by averagineprecursor_peak_calculator_DIY_averagine
rankify numeric vector via ftFileWriterrankyfify
read MS1 scans with scanNumber as indexreadAllScanMS1
read MS2 scans with scanNumber as indexreadAllScanMS2
readFilesScansTopPSMsreadFilesScansTopPSMs
readFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .sip files of one .FT2 filereadFilesScansTopPSMsFromOneFT2
read FT file headerreadFTheader
Read spectra from .mgf filereadMgf
Read MS1 spectra from .mzML filereadMzmlMS1
Read MS2 spectra from .mzML filereadMzmlMS2
readOneScanMS1readOneScanMS1
readOneScanMS2readOneScanMS2
Read PSM table from .pepXML filereadPepXMLtable
Read PSM TSV FilereadPSMtsv
read MS1 scans with scanNumber as index in a rangereadScansMS1
read MS1 scans with scanNumber as index in a vectorreadScansMS1Vector
read MS2 scans with scanNumber as index in a rangereadScansMS2
read MS2 scans with scanNumber as index in a vectorreadScansMS2Vector
readSipreadSip
readSipsreadSips
readSpe2PepreadSpe2Pep
readSpe2PepFilesScansTopPSMs read each scan's top PSMs from multiple .Spe2Pep.txt filesreadSpe2PepFilesScansTopPSMs
readSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 filereadSpe2PepFilesScansTopPSMsFromEachFT2Parallel
readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParalle read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 filereadSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel
readSpe2PepFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .Spe2PepFile.txt files of one .FT2 filereadSpe2PepFilesScansTopPSMsFromOneFT2
readSpe2PepsreadSpe2Peps
Simple residue peak calculator of user defined isotopic distribution of one residueresidue_peak_calculator_DIY
scoreIntensityscoreIntensity
scoreIntensityByCrossEntropyscoreIntensityByCE
scorePSMscorePSM
scorePSMsimple Score a PSM without isotopic envelope shape modelingscorePSMsimple
Summarize SIP percent for PSMssummaryPSMsipPCT
write all MS1 scans has chargewriteAllScanMS1
write all MS2 scans has chargewriteAllScanMS2
writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file and write them to one tsv filewriteSpe2PepFilesScansTopPSMsFromEachFT2Parallel