Package: Aerith 1.1.1

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_1.1.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Aerith/json (API)

# Install 'Aerith' in R:
install.packages('Aerith', repos = c('https://bioc.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

7.12 score 5 stars 54 scripts 86 exports 39 dependencies

Last updated from:562352cca9. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING239
linux-devel-arm64NOTE240
linux-devel-x86_64NOTE268
source / vignettesOK432
linux-release-arm64NOTE238
linux-release-x86_64NOTE308
macos-release-arm64NOTE142
macos-release-x86_64NOTE379
macos-oldrel-arm64NOTE185
macos-oldrel-x86_64NOTE514
windows-develNOTE301
windows-releaseNOTE283
windows-oldrelNOTE232
wasm-releaseOK212

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:BiobaseBiocGenericsbiocmakeclicpp11data.tabledir.expirydplyrfarverfilelockgenericsggplot2ggrepelgluegtableisobandlabelinglifecyclemagrittrmzRncdf4pillarpkgconfigProtGenericsR6RColorBrewerRcppRhdf5librlangS7scalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr

Aerith
Abstract | Introduction | Vignette contents | Input Data Format | PSM annotation and visualization | Simulation and visualization of isotopic envelopes for metabolites | Simulation and visualization of isotopic envelopes for peptides | Score functions for PSM evaluation | Visualization of SIP proteomic result | S4 classes in Aerith
Rendered fromAerith.Rmdusingknitr::rmarkdown

Last update: 2026-05-05
Started: 2025-06-14

Input Data Format and File Handling in Aerith
Overview | What Makes Aerith Unique | Data Format Overview | File Format Conversion | Converting Raw Files to Supported Formats | Working with FT1 and FT2 Files | Reading MS1 and MS2 Scan Data | Creating Subset Files for Testing and Development | Working with mzML Files | Working with MGF Files | Processing Peptide Identification Results | Reading pepXML Files | Working with Sipros Output Files | Reading PSM Files from Sipros | Quality Control and Data Visualization | Total Ion Current (TIC) Analysis | Instrument Performance Analysis | Advanced Precursor Analysis | Summary | Key Strengths of Aerith: | Best Practices Summary:
Rendered fromInput-data-format.Rmdusingknitr::rmarkdown

Last update: 2026-05-05
Started: 2025-03-11

PSM Annotation and Visualization
Introduction | Overview of PSM Annotation | Advantages of Aerith | Analysis of Unlabeled PSM at Natural ^13^C Abundance (1.07%) | Fragment Ion Annotation at MS2 Level | Interactive PSM Annotation Visualization | Comprehensive Fragment Analysis with Theoretical Overlays | Precursor Ion Analysis at MS1 Level | Analysis of Heavily Labeled PSM at 50% ^13^C Incorporation | Fragment Ion Annotation in Labeled Samples | Visualization of Heavy Labeling Effects | Theoretical vs Observed Fragment Comparison in Heavy Labeling | Precursor Analysis Under Heavy Labeling Conditions | High-Throughput Batch Processing of PSMs | Automated Batch Analysis Workflow | Summary and Best Practices | Key Takeaways | Parameter Selection Guidelines
Rendered fromPSM-annotation-and-visualization.Rmdusingknitr::rmarkdown

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

Score function test of PSM
Overview of scoring functions | Unlabeled PSM at 1.07% ^13^C | Labeled PSM at 50% ^13^C | Annotate B and Y ion fragments | Guidance on parameter selection and interpretation | Why Aerith stands out
Rendered fromScore-function-test-of-PSM.Rmdusingknitr::rmarkdown

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

Theoretic spectra generation of SIP-labeled compound
Overview | Monte Carlo method | FFT-based algorithm | Summary
Rendered fromTheoretic-spectra-generation-of-SIP-labeled-compound.Rmdusingknitr::rmarkdown

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

Theoretic spectra generation of SIP-labeled peptide
Overview | Unlabeled Spectra | Get precursor mass | Plot precursor's theoretical spectra | Get peptide fragments' mass | Plot peptide fragments' theoretical spectra | Labeled Spectra
Rendered fromTheoretic-spectra-generation-of-SIP-labeled-peptide.Rmdusingknitr::rmarkdown

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

Visualization of SIP proteomic result
Overview of SIP Percent Summaries | Summarize SIP percent for PSMs | Visualizing SIP Percent Distributions | Plot the distribution of SIP percent for PSMs | Why Aerith Fits Modern SIP Proteomics
Rendered fromVisualization-of-SIP-proteomic-result.Rmdusingknitr::rmarkdown

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