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

## Documentation for package ‘Aerith’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

AAspectra-class | AAspectra S4 class for annotated mass spectra
annotatePrecursor | annotatePrecursor
annotatePSM | annotatePSM
BYion_peak_calculator_DIY | BY Ion Peak Calculator with User-Defined Isotopic Distribution
calBYAtomCountAndBaseMass | Simple calculator of C H O N P S atom count and mass without isotope of B Y ions
calPepAtomCount | Simple calculator of C H O N P S atom count of peptide
calPepNeutronMass | Simple calculator neutron mass by average delta mass of each isotope
calPepPrecursorMass | Simple calculator of peptide precursor mass by binomial NP
cal_isotope_numbers | Calculate Isotope Numbers in natural abundance
cal_isotope_numbers_SIP | Calculate Isotope Numbers for SIP
cal_isotope_peaks_fft | Calculate Isotope Peaks using FFT
denoiseOneMS2ScanHasCharge | denoise one MS2 scan has charge
extractPSMfeatures | extractPSMfeatures extract featueres of top PSMs from multiple .Spe2Pep.txt files
extractPSMfeaturesTargetAndDecoy | extractPSMfeaturesTargetAndDecoy extract featueres of top PSMs from target and decoy .Spe2Pep.txt files
extractPSMfeaturesTargetAndDecoytoPercolatorPin | extractPSMfeaturesTargetAndDecoytoPercolatorPin extract featueres of top PSMs from target and decoy .Spe2Pep.txt files to pecorlator pin format
generateCFGs | generateCFGs
generateOneCFG | generateOneCFG
getFilterThreshold | getFilterThreshold
getFilterThresholdTopPSMs | getFilterThresholdTopPSMs get filter threshold of top PSMs of each scan from multiple .sip file
getFilterThresholdTopPSMsSpe2Pep | getFilterThresholdTopPSMsSpe2Pep get filter threshold of top PSMs of each scan from multiple .sip file
getMZ | add MZ to spectra data.frame
getPrecursorSpectra | Get AAspectra object of precursor from AA sequence with natural SIP abundance
getRealScan | Convert one scan with charges=1 normalized by highest peak in scans list of ft file to AAspectra class
getRealScanFromList | Convert one scan in list format to AAspectra class
getRealScans | Get real scans from a scans list of one FT file with charges converted to 1 and intensities normalized by the highest peak.
getRealScansWithCharges | get real scans with real charges and raw intensities from scans list of one ft file
getRealScanWithCharge | Convert one scan in scans with real charges and raw intensities from list of scans of ft file to AAspectra class
getRetentionTimeAndPrecursorInfo | get retention time and precursor mass from scans list of ft file
getSipBYionSpectra | Get AAspectra object of B and Y ions from AA sequence with labeled SIP abundance
getSipPrecursorSpectra | Get AAspectra object of precursor from AA sequence with labeled SIP abundance
getTIC | get TIC and retention time from scans list of ft file
getUnfilteredPeptides | getUnfilteredPeptides
getUnfilteredPSMs | getUnfilteredPSMs
plot-method | Plot an AAspectra object
plotFilteredPCTIntensitySummary | Plot decoy-filtered PSMs' PCT and intensity summary by each input file
plotMolecularFFTisotopes | Plot Molecular isotopes without fine structure by FFT algorithm
plotMolecularIsotopes | Plot Molecular Isotopes with fine structure by Montecarlo algorithm
plotPrecursorAnnotation | plot precursor annotation
plotPrecursorMzFrequency | Plot precursor MZ frequency per 5 per minute of MS2
plotProSipPct | plot the distribution of SIP percent of proteins
plotPSMannotation | plot PSM annotation
plotPSMs | plot PSMs from FT2 files and PSM results
plotPSMsipPCT | Plot the distribution of SIP percent for PSMs
plotRealScan | plot real scan layer under the B Y ion peaks
plotScanFrequency | Plot scan frequency
plotScanFrequencyMS2 | Plot scan frequency layer of MS2
plotScoreDistribution | plot the score of PSMs at different charge and mass error
plotSipBYionLabel | Draw AAspectra MS plot with B Y ion Labels
plotSIPfilteredPCTIntensityBySample | Plot SIP-filtered PCT and intensity summary by each input file
plotTIC | Plot TIC of MS1 or MS2
precursor_peak_calculator | Precursor Peak Calculator
precursor_peak_calculator_DIY | Precursor Peak Calculator with User-Defined Isotopic Distribution
precursor_peak_calculator_DIY_averagine | Simple peak calculator of user defined isotopic distribution of one peptide by averagine
rankyfify | rankify numeric vector via ftFileWriter
readAllScanMS1 | read MS1 scans with scanNumber as index
readAllScanMS2 | read MS2 scans with scanNumber as index
readFilesScansTopPSMs | readFilesScansTopPSMs
readFilesScansTopPSMsFromOneFT2 | readFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .sip files of one .FT2 file
readFTheader | read FT file header
readMgf | Read spectra from .mgf file
readMzmlMS1 | Read MS1 spectra from .mzML file
readMzmlMS2 | Read MS2 spectra from .mzML file
readOneScanMS1 | readOneScanMS1
readOneScanMS2 | readOneScanMS2
readPepXMLtable | Read PSM table from .pepXML file
readPSMtsv | Read PSM TSV File
readScansMS1 | read MS1 scans with scanNumber as index in a range
readScansMS1Vector | read MS1 scans with scanNumber as index in a vector
readScansMS2 | read MS2 scans with scanNumber as index in a range
readScansMS2Vector | read MS2 scans with scanNumber as index in a vector
readSip | readSip
readSips | readSips
readSpe2Pep | readSpe2Pep
readSpe2PepFilesScansTopPSMs | readSpe2PepFilesScansTopPSMs read each scan's top PSMs from multiple .Spe2Pep.txt files
readSpe2PepFilesScansTopPSMsFromEachFT2Parallel | readSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file
readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel | readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParalle read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file
readSpe2PepFilesScansTopPSMsFromOneFT2 | readSpe2PepFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .Spe2PepFile.txt files of one .FT2 file
readSpe2Peps | readSpe2Peps
residue_peak_calculator_DIY | Simple residue peak calculator of user defined isotopic distribution of one residue
scoreIntensity | scoreIntensity
scoreIntensityByCE | scoreIntensityByCrossEntropy
scorePSM | scorePSM
scorePSMsimple | scorePSMsimple Score a PSM without isotopic envelope shape modeling
summaryPSMsipPCT | Summarize SIP percent for PSMs
writeAllScanMS1 | write all MS1 scans has charge
writeAllScanMS2 | write all MS2 scans has charge
writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel | writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file and write them to one tsv file