Package 'Aerith'

Title: visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics
Description: 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] (ORCID: <https://orcid.org/0009-0005-4591-2366>)
Maintainer: Yi Xiong <[email protected]>
License: GPL-3
Version: 1.1.1
Built: 2026-06-04 10:22:24 UTC
Source: https://github.com/bioc/Aerith

Help Index

AAspectra S4 class for annotated mass spectra

Description

Unified container storing theoretical or observed spectra, their charge states, and the associated peptide or compound identifier.

Details

Instances of this class are typically created by helper constructors like getPrecursorSpectra(), getSipPrecursorSpectra(), or converted from raw scans with getRealScan(). The class underpins downstream plotting and annotation methods.

Slots

spectra

A data.frame with columns such as Mass, MZ, Prob, Kind, and Charge, holding peaks and metadata.

charges

Numeric vector of precursor charge states carried alongside spectra.

AAstr

Character string containing the peptide sequence or compound label used to generate the spectrum.

See Also

getPrecursorSpectra(), getSipPrecursorSpectra(), getSipBYionSpectra(), plot,AAspectra,missing-method

Examples

AAstr <- "KHRIP"
spectra <- getPrecursorSpectra(AAstr, 1:2)
class(spectra)

annotatePrecursor

Description

annotatePrecursor

Usage

annotatePrecursor(
  realMZ,
  realIntensity,
  realCharge,
  pepSeq,
  charge,
  Atom,
  Prob,
  isoCenter = 0,
  isoWidth = 0,
  calScores = FALSE
)

Arguments

realMZ

mz vector in precursor scan
realIntensity

intensity vector in precursor scan
realCharge

charge vector in precursor scan
pepSeq

a string of peptide
charge

charge of precursor ion in consideration
Atom

"C13" or "N15"
Prob

its SIP abundance (0.0~1.0)
isoCenter

isolation window center, set it 0 as default if not filtering by isolation window
isoWidth

isolation window width, set it 0 as default if not filtering by isolation window
calScores

FALSE as default, calculate matched spectra entropy score or not

Value

a List about matched precursor isotopic peaks information

Examples

realMZ <- c(
  894.9413, 895.4429, 895.9444, 896.3896, 896.4448, 896.9463,
  897.3890, 897.8896, 898.3930, 898.4734, 901.8851, 902.4465,
  902.9483, 903.4498, 903.9504, 910.8968, 911.4449, 912.3784
)
realIntensity <- c(
  16660537.0, 12344664.0, 6128400.5, 1448961.1, 1614148.1, 713238.8,
  1999402.4, 1124157.4, 567865.2, 647140.8, 709644.2, 7805729.0,
  8421993.0, 3200114.2, 1286055.5, 620246.8, 540861.6, 1079918.5
)
realCharge <- c(2, 2, 2, 0, 2, 2, 2, 2, 2, 0, 0, 2, 2, 2, 2, 0, 0, 2)
anno <- annotatePrecursor(
  realMZ, realIntensity, realCharge,
  "GITINTSHVEYDTPTR", 2, "C13",
  0.01, 902.4471, 20, TRUE
)

annotatePSM

Description

annotatePSM

Usage

annotatePSM(
  realMZ,
  realIntensity,
  realCharge,
  pepSeq,
  charges,
  Atom,
  Prob,
  isoCenter = 0,
  isoWidth = 0,
  calScores = FALSE
)

Arguments

realMZ

mz vector in MS2 scan
realIntensity

intensity vector in MS2 scan
realCharge

charge vector in MS2 scan
pepSeq

a string of peptide
charges

charges of product ions in consideration
Atom

"C13" or "N15"
Prob

its SIP abundance (0.0~1.0)
isoCenter

isolation window center, set it 0 as default if not remove peaks in isolation window
isoWidth

isolation window width, set it 0 as default if not remove peaks in isolation window
calScores

FALSE as default, calculate WDP MVH Xcor scores or not

Value

a List about matched peaks information of this PSM

Examples

demo_file <- system.file("extdata", "107728.FT2", package = "Aerith")
scan1 <- readOneScanMS2(ftFile = demo_file, 107728)
anno <- annotatePSM(
  scan1$peaks$mz, scan1$peaks$intensity,
  scan1$peaks$charge,
  "HSQVFSTAEDNQSAVTIHVLQGER", 1:2, "C13",
  0.0107, 886.65, 4.0, TRUE
)

BY Ion Peak Calculator with User-Defined Isotopic Distribution

Description

This function calculates the isotopic distribution of B and Y ions for a given amino acid string with a user-defined isotopic distribution and returns a DataFrame containing the mass, probability, and type of each ion.

Usage

BYion_peak_calculator_DIY(AAstr, Atom, Prob)

Arguments

AAstr

A string representing the amino acid sequence.
Atom

A string representing the isotope ("C13", "N15", "H2", "O18", "S34").
Prob

A double representing the abundance of the specified isotope (0.0 to 1.0).

Value

A DataFrame with three columns: "Mass" containing the mass of each ion, "Prob" containing the probability of each ion, and "Kind" indicating whether the ion is a B or Y ion.

Examples

# Example usage
df <- BYion_peak_calculator_DIY("PEPTIDE", "C13", 0.2)
df <- BYion_peak_calculator_DIY("PEPTIDE", "N15", 0.5)

Calculate Isotope Numbers in natural abundance

Description

This function calculates the isotope numbers for a given chemical formula using a Monte Carlo simulation approach.

Usage

cal_isotope_numbers(formula, num_simulations = 10000)

Arguments

formula

A character string representing the chemical formula.
num_simulations

An integer specifying the number of simulations to run. Default is 10,000.

Value

A data frame containing the results of the simulations.

Examples

cal_isotope_numbers("C6H12O6")
cal_isotope_numbers("CF3COOH", num_simulations = 5000)

Calculate Isotope Numbers for SIP

Description

This function calculates the isotope numbers for Stable Isotope Probing (SIP) based on a given chemical formula using a Monte Carlo simulation approach.

Usage

cal_isotope_numbers_SIP(formula, num_simulations = 10000, ...)

Arguments

formula

A character string representing the chemical formula, "C6H12O6" for example.
num_simulations

An integer specifying the number of simulations to run. Default is 10,000.
...

Additional arguments passed to the function, C13=0.5 for example to set the abundance of C13 to 0.5.

Value

A dataframe containing the results of the isotope number and mass calculations.

Examples

cal_isotope_numbers_SIP("C6H12O6")
cal_isotope_numbers_SIP("C6H12O6", num_simulations = 10000, C13 = 0.5)

Calculate Isotope Peaks using FFT

Description

This function calculates the isotope peaks for a given chemical formula using Fast Fourier Transform (FFT). It approximates the delta mass of isotopes is one neutron mass and ignore the fine structure of isotopes.

Usage

cal_isotope_peaks_fft(formula, N_width = 100, min_abundance = 1e-04, ...)

Arguments

formula

A character string representing the chemical formula.
N_width

An integer specifying the width of the isotope envelope in FFT. Default is 100. Wider isotopic envolope will require larger N_width.
min_abundance

A numeric value specifying the minimum abundance threshold for the peaks. Default is 0.0001.
...

Additional arguments passed to the function. For example C13=0.5 will change the abundance of C13 to 0.5 and adjust the abundance of C12 accordingly.

Value

data.frame A data frame containing the calculated isotope peaks mass and their abundances.

Examples

# Example usage:
cal_isotope_peaks_fft("C6H12O6")
cal_isotope_peaks_fft("C6H12O6", N_width = 200, min_abundance = 0.001, C13 = 0.5)

Simple calculator of C H O N P S atom count and mass without isotope of B Y ions

Description

Simple calculator of C H O N P S atom count and mass without isotope of B Y ions

Usage

calBYAtomCountAndBaseMass(AAstrs)

Arguments

AAstrs

a CharacterVector of peptides

Value

a list of data.frame of C H O N P S atom count and each data.frame is for one peptide

Examples

peps <- calBYAtomCountAndBaseMass(c("HK~FL","AD!CH","~ILKMV"))

Simple calculator of C H O N P S atom count of peptide

Description

Simple calculator of C H O N P S atom count of peptide

Usage

calPepAtomCount(AAstrs)

Arguments

AAstrs

a CharacterVector of peptides

Value

a dataframe of C H O N P S atom count each row is for one peptide

Examples

df <- calPepAtomCount(c("HKFL","ADCH"))

Simple calculator neutron mass by average delta mass of each isotope

Description

Simple calculator neutron mass by average delta mass of each isotope

Usage

calPepNeutronMass(AAstrs, Atom, Probs)

Arguments

AAstrs

a CharacterVector of peptides
Atom

a Character of "C13", "H2", "O18", "N15", or "S34"
Probs

a NumericVector with the same length of AAstr for SIP abundances

Value

a vector of peptide neutron masses

Examples

masses <- calPepNeutronMass(c("HKFL", "ADCH"), "C13", c(0.2, 0.3))

Simple calculator of peptide precursor mass by binomial NP

Description

Simple calculator of peptide precursor mass by binomial NP

Usage

calPepPrecursorMass(AAstrs, Atom, Probs)

Arguments

AAstrs

a CharacterVector of peptides
Atom

a Character of "C13", "H2", "O18", "N15", or "S34"
Probs

a NumericVector with the same length of AAstr for SIP abundances

Value

a vector of peptide precursor masses

Examples

masses <- calPepPrecursorMass(c("HKFL", "ADCH"), "C13", c(0.2, 0.3))

denoise one MS2 scan has charge

Description

denoise one MS2 scan has charge

Usage

denoiseOneMS2ScanHasCharge(scanList, window, step, threshold)

Arguments

scanList

a list of one MS2 scan has charge
window

a float of mz window size for denoise
step

a float of mz step for denoise
threshold

a float of top N threshold for denoise

Value

a denoised MS2 scan has charge

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
ft2 <- readAllScanMS2(demo_file)
plot(getRealScanFromList(ft2[["1346"]]))
ms2 <- denoiseOneMS2ScanHasCharge(ft2[["1346"]], 100, 10, 5)
plot(getRealScanFromList(ms2))

extractPSMfeatures extract featueres of top PSMs from multiple .Spe2Pep.txt files

Description

extractPSMfeatures extract featueres of top PSMs from multiple .Spe2Pep.txt files

Usage

extractPSMfeatures(Spe2PepFilePath, topN, ftFilepath, ThreadNumber = 3L)

Arguments

Spe2PepFilePath

a full path with .Spe2Pep.txt files in it
topN

store top N PSMs of each scan of one .FT2 file
ftFilepath

a full path with .FT1 and .FT2 files in it
ThreadNumber

read ThreadNumber of FT file at the same time, it will increase ram usage

Details

Set OpenMP stack size to avoid stack overflow in parallel processing before loading Aerith package: Sys.setenv(OMP_STACKSIZE = "16M") Sys.setenv(OMP_NUM_THREADS = parallel::detectCores())

Value

A named list of data frames, each containing the extracted PSM features from the corresponding .Spe2Pep.txt file.

Examples

tmp <- tempdir()
target_dir <- file.path(tmp, "target")
dir.create(target_dir, showWarnings = FALSE)
target_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(target_file, file.path(target_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
ft_dir <- file.path(tmp, "ft")
dir.create(ft_dir, showWarnings = FALSE)
ft_file <- system.file("extdata", "demo_target_decoy.FT1.rds", package = "Aerith")
file_content <- readRDS(ft_file)
writeLines(file_content, file.path(ft_dir, "Pan_052322_X13.FT1"))
print(list.files(c(ft_dir, target_dir), full.names = TRUE, recursive = TRUE))
psm <- extractPSMfeatures(target_dir, 5, ft_dir, 3)

extractPSMfeaturesTargetAndDecoy extract featueres of top PSMs from target and decoy .Spe2Pep.txt files

Description

extractPSMfeaturesTargetAndDecoy extract featueres of top PSMs from target and decoy .Spe2Pep.txt files

Usage

extractPSMfeaturesTargetAndDecoy(
  targetPath,
  decoyPath,
  topN,
  ftFilepath,
  ThreadNumber = 3L
)

Arguments

targetPath

a full path with target .Spe2PepFile.txt files in it
decoyPath

a full path with decoy .Spe2PepFile.txt files in it
topN

store top N PSMs of each scan of one .FT2 file
ftFilepath

a full path with .FT1 and .FT2 files in it
ThreadNumber

read ThreadNumber of FT file at the same time, it will increase ram usage

Details

Set OpenMP stack size to avoid stack overflow in parallel processing before loading Aerith package: Sys.setenv(OMP_STACKSIZE = "16M") Sys.setenv(OMP_NUM_THREADS = parallel::detectCores())

Value

the PSMs in a dataframe in a list

Examples

tmp <- tempdir()
target_dir <- file.path(tmp, "target")
dir.create(target_dir, showWarnings = FALSE)
target_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(target_file, file.path(target_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
decoy_dir <- file.path(tmp, "decoy")
dir.create(decoy_dir, showWarnings = FALSE)
decoy_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(decoy_file, file.path(decoy_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
ft_dir <- file.path(tmp, "ft")
dir.create(ft_dir, showWarnings = FALSE)
ft_file <- system.file("extdata", "demo_target_decoy.FT1.rds", package = "Aerith")
file_content <- readRDS(ft_file)
writeLines(file_content, file.path(ft_dir, "Pan_052322_X13.FT1"))
print(list.files(c(ft_dir, target_dir, decoy_dir), full.names = TRUE, recursive = TRUE))
psm <- extractPSMfeaturesTargetAndDecoy(target_dir, decoy_dir, 3, ft_dir, 3)

extractPSMfeaturesTargetAndDecoytoPercolatorPin extract featueres of top PSMs from target and decoy .Spe2Pep.txt files to pecorlator pin format

Description

extractPSMfeaturesTargetAndDecoytoPercolatorPin extract featueres of top PSMs from target and decoy .Spe2Pep.txt files to pecorlator pin format

Usage

extractPSMfeaturesTargetAndDecoytoPercolatorPin(
  targetPath,
  decoyPath,
  topN,
  ftFilepath,
  ThreadNumber = 3L,
  doProteinInference = FALSE,
  fileName = "a.pin"
)

Arguments

targetPath

a full path with target .Spe2PepFile.txt files in it
decoyPath

a full path with decoy .Spe2PepFile.txt files in it
topN

store top N PSMs of each scan of one .FT2 file
ftFilepath

a full path with .FT1 and .FT2 files in it
ThreadNumber

read ThreadNumber of FT file at the same time, it will increase ram usage
doProteinInference

out put protein inference format or only PSM format
fileName

output path of the percolator tsv file

Details

Set OpenMP stack size to avoid stack overflow in parallel processing before loading Aerith package: Sys.setenv(OMP_STACKSIZE = "16M") Sys.setenv(OMP_NUM_THREADS = parallel::detectCores())

Value

NULL (invisibly).

Examples

tmp <- tempdir()
target_dir <- file.path(tmp, "target")
dir.create(target_dir, showWarnings = FALSE)
target_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(target_file, file.path(target_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
decoy_dir <- file.path(tmp, "decoy")
dir.create(decoy_dir, showWarnings = FALSE)
decoy_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(decoy_file, file.path(decoy_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
ft_dir <- file.path(tmp, "ft")
dir.create(ft_dir, showWarnings = FALSE)
ft_file <- system.file("extdata", "demo_target_decoy.FT1.rds", package = "Aerith")
file_content <- readRDS(ft_file)
writeLines(file_content, file.path(ft_dir, "Pan_052322_X13.FT1"))
pin_path <- file.path(tmp, "a.pin")
extractPSMfeaturesTargetAndDecoytoPercolatorPin(target_dir, decoy_dir, 3, ft_dir, 3, FALSE, pin_path)
print(list.files(c(ft_dir, target_dir, decoy_dir), full.names = TRUE, recursive = TRUE))
print(file.info(pin_path))

generateCFGs

Description

generateCFGs

Usage

generateCFGs(cfgPath, outPath, element)

Arguments

cfgPath

a full path of .cfg file
outPath

a full path for .cfg file output
element

a string of element name, "N" for example

Value

a bool value if generate succeed or not

Examples

cfg <- system.file("extdata", "SiprosConfig.cfg", package = "Aerith")
tmp <- tempdir()
tmp <- file.path(tmp, "configs")
generateCFGs(cfg, tmp, "N")
list.files(tmp, full.names = TRUE)

generateOneCFG

Description

generateOneCFG

Usage

generateOneCFG(cfgPath, outPath, element, pct, center, width)

Arguments

cfgPath

a full path of .cfg file
outPath

a full path for .cfg file output
element

a string of element name, "N" for example
pct

a integer of element SIP abundance
center

a integer of mass window center
width

a integer of mass half window width

Value

a bool value if generate succeed or not

Examples

cfg <- system.file("extdata", "SiprosConfig.cfg", package = "Aerith")
tmp <- tempdir()
tmp <- file.path(tmp, "configs")
generateOneCFG(cfg, tmp, "N", 50, 0, 2)
list.files(tmp, full.names = TRUE)

getFilterThreshold

Description

getFilterThreshold

Usage

getFilterThreshold(workingPath, OverallThreshold)

Arguments

workingPath

a full path with .sip files in it
OverallThreshold

FDR thredhold of peptides

Value

a dataframe about filter threshold and FDR results

Examples

demo_dir <- system.file("extdata", package = "Aerith")
getFilterThreshold(demo_dir, 0.01)

getFilterThresholdTopPSMs get filter threshold of top PSMs of each scan from multiple .sip file

Description

getFilterThresholdTopPSMs get filter threshold of top PSMs of each scan from multiple .sip file

Usage

getFilterThresholdTopPSMs(workingPath, OverallThreshold, topN)

Arguments

workingPath

a full path with .sip files in it
OverallThreshold

FDR thredhold of peptides
topN

store top N PSMs of each scan of one .FT file

Value

a dataframe about filter threshold and FDR results

Examples

demo_dir <- system.file("extdata", package = "Aerith")
re <- getFilterThresholdTopPSMs(demo_dir, 0.01, 3)
re$threshold
head(re$topPSMs)

getFilterThresholdTopPSMsSpe2Pep get filter threshold of top PSMs of each scan from multiple .sip file

Description

getFilterThresholdTopPSMsSpe2Pep get filter threshold of top PSMs of each scan from multiple .sip file

Usage

getFilterThresholdTopPSMsSpe2Pep(
  workingPath,
  OverallThreshold,
  topN,
  decoyPrefix
)

Arguments

workingPath

a full path with .Spe2Pep files in it
OverallThreshold

FDR thredhold of peptides
topN

store top N PSMs of each scan of one .FT file
decoyPrefix

the prefix of decoy sequence

Value

a dataframe about filter threshold and FDR results, rows of ", 0, 0 ,0" means cannot find threshold at this charge

Examples

tmp <- tempdir()
sip_dir <- file.path(tmp, "sip")
dir.create(sip_dir)
demo_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000target.Spe2Pep.txt"))
demo_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000decoy.Spe2Pep.txt"))
list.files(sip_dir, full.names = TRUE)
a <- getFilterThresholdTopPSMsSpe2Pep(sip_dir, 1, 3, "Decoy_")
a$threshold

add MZ to spectra data.frame

Description

add MZ to spectra data.frame

Usage

getMZ(spectra, charges = c(1, 2))

Arguments

spectra

a dataframe of spectra
charges

ion charges

Value

a dataframe of spectra

Examples

spectra <- precursor_peak_calculator("KHRIP")
spectra <- getMZ(spectra, 1:2)

Get AAspectra object of precursor from AA sequence with natural SIP abundance

Description

Get AAspectra object of precursor from AA sequence with natural SIP abundance

Usage

getPrecursorSpectra(AAstr, charges = c(1, 2))

Arguments

AAstr

Amino acid string
charges

Integer vector of charges. Default is 1:2

Value

AAspectra object

Examples

getPrecursorSpectra("KHRIP", 1:2)

Convert one scan with charges=1 normalized by highest peak in scans list of ft file to AAspectra class

Description

Convert one scan with charges=1 normalized by highest peak in scans list of ft file to AAspectra class

Usage

getRealScan(scanNumber, ft)

Arguments

scanNumber

ScanNumber of one scan
ft

Scans list of ft file

Value

AAspectra object

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getRealScan(1388, a)
plot(b)

Convert one scan in list format to AAspectra class

Description

Convert one scan in list format to AAspectra class

Usage

getRealScanFromList(scan)

Arguments

scan

one scan in list format

Value

AAspectra object

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getRealScanFromList(a[[1]])
plot(b)

Get real scans from a scans list of one FT file with charges converted to 1 and intensities normalized by the highest peak.

Description

Get real scans from a scans list of one FT file with charges converted to 1 and intensities normalized by the highest peak.

Usage

getRealScans(ft, scanNumbers)

Arguments

ft

A list of scans from one FT file.
scanNumbers

An integer vector of scan numbers of PSMs.

Value

A list of AAspectra objects representing the real scans.

Examples

scanNumbers <- c("2596", "8182")
demo_file <- system.file("extdata", "X13_4068_2596_8182.FT2", package = "Aerith")
ft2 <- readAllScanMS2(demo_file)
realScans <- getRealScans(ft2, scanNumbers)

get real scans with real charges and raw intensities from scans list of one ft file

Description

get real scans with real charges and raw intensities from scans list of one ft file

Usage

getRealScansWithCharges(ft, scanNumbers)

Arguments

ft

Scans list of one ft file
scanNumbers

Integer vector of scan number of PSMs

Value

List of AAspectra objects of real scans

Examples

scanNumbers <- c("2596", "8182")
demo_file <- system.file("extdata", "X13_4068_2596_8182.FT2", package = "Aerith")
ft2 <- readAllScanMS2(demo_file)
realScans <- getRealScansWithCharges(ft2, scanNumbers)

Convert one scan in scans with real charges and raw intensities from list of scans of ft file to AAspectra class

Description

Convert one scan in scans with real charges and raw intensities from list of scans of ft file to AAspectra class

Usage

getRealScanWithCharge(scanNumber, ft)

Arguments

scanNumber

Integer. The scan number of one scan.
ft

List. The list of scans from an ft file.

Value

AAspectra object containing the scan data.

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getRealScanWithCharge(1388, a)
head(slot(b, "spectra"))

get retention time and precursor mass from scans list of ft file

Description

get retention time and precursor mass from scans list of ft file

Usage

getRetentionTimeAndPrecursorInfo(ft)

Arguments

ft

Scans list of ft file

Value

A data.frame of retention time and precursor mass

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getRetentionTimeAndPrecursorInfo(a)
rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
a <- readAllScanMS1(demo_file)
b <- getRetentionTimeAndPrecursorInfo(a)

Get AAspectra object of B and Y ions from AA sequence with labeled SIP abundance

Description

Get AAspectra object of B and Y ions from AA sequence with labeled SIP abundance

Usage

getSipBYionSpectra(
  AAstr,
  Atom = "C13",
  Prob = 0.0107,
  charges = 1,
  precursorCharges = 2
)

Arguments

AAstr

Amino acide string
Atom

"C13" or "N15". Default is "C13"
Prob

C13 or N15's abundance. Default is 0.0107
charges

NumericVector of product ion's charge. Default is 1:2
precursorCharges

NumericVector of precursor's charge. Default is 2

Value

AAspectra object

Examples

# add precursor
a <- getSipBYionSpectra("KHRIPCDRK", "C13", 0.05, 1:2, 2)
tail(slot(a, "spectra"))
# not add precursor
a <- getSipBYionSpectra("KHRIPCDRK", "C13", 0.05, 1:2, 0)
tail(slot(a, "spectra"))

Get AAspectra object of precursor from AA sequence with labeled SIP abundance

Description

Get AAspectra object of precursor from AA sequence with labeled SIP abundance

Usage

getSipPrecursorSpectra(AAstr, Atom = "C13", Prob = 0.0107, charges = c(1, 2))

Arguments

AAstr

Amino acide string
Atom

"C13" or "N15". Default is "C13"
Prob

C13 or N15's abundance. Default is 0.0107
charges

Integer vector of charges. Default is 1:2

Value

AAspectra object

Examples

getSipPrecursorSpectra("KHRIPCDRK", "C13", 0.05, 1:3)

get TIC and retention time from scans list of ft file

Description

TIC: total ion chromatogram.

Usage

getTIC(ft)

Arguments

ft

Scans list of ft file

Value

A data.frame of TIC, relative TIC and retention time

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getTIC(a)

getUnfilteredPeptides

Description

getUnfilteredPeptides

Usage

getUnfilteredPeptides(workingPath)

Arguments

workingPath

a full path with .sip files in it

Value

a dataframe of unique peptides and whether it is decoy sequence

Examples

demo_dir <- system.file("extdata", package = "Aerith")
head(getUnfilteredPeptides(demo_dir))

getUnfilteredPSMs

Description

getUnfilteredPSMs

Usage

getUnfilteredPSMs(sipPath, ftPath, topN)

Arguments

sipPath

a full path with .sip files in it
ftPath

a full path with .ft files in it
topN

store top N PSMs of each scan of one .FT file

Value

data.frame of PSMs

Examples

demo_dir <- system.file("extdata", package = "Aerith")
head(getUnfilteredPSMs(demo_dir, demo_dir, 10))

Plot an AAspectra object

Description

S4 plot method producing a ggplot2 spectrum for an AAspectra object.

Usage

## S4 method for signature 'AAspectra,missing'
plot(x, y, linewidth = 0.1, ...)

Arguments

x

AAspectra object.
y

(ignored, must be missing)
linewidth

Numeric width of MS peaks. Default 0.1.
...

Passed on (currently unused).

Value

A ggplot2 object.

See Also

AAspectra

Examples

a <- getPrecursorSpectra("KHRIP", 2)
plot(a) +
    ggplot2::scale_x_continuous(breaks = seq(324, 329, by = 0.5)) +
    ggplot2::geom_linerange(linewidth = 0.2)

Plot decoy-filtered PSMs' PCT and intensity summary by each input file

Description

This function reads all filtered PSM files in from output directory of Sipros 5, combines them, filters for labeled PSMs, extracts file names, computes log2 intensities, and generates a hexbin plot faceted by each input file.

Usage

plotFilteredPCTIntensitySummary(
  psms_dir = "psms/",
  output_file = "decoy_filtered_PCT_and_intensity_summary_by_file.pdf",
  width = 16,
  height = 12
)

Arguments

psms_dir

Directory containing filtered PSM files (default: "psms/").
output_file

Output PDF file name for the plot.
width

Width of the output PDF (default: 16).
height

Height of the output PDF (default: 12).

Value

A ggplot2 object representing the hexbin plot.

Plot Molecular isotopes without fine structure by FFT algorithm

Description

This function plots the molecular isotopes generated by Fast Fourier Transform (FFT).

Usage

plotMolecularFFTisotopes(
  isotope_numbers,
  charge = 1,
  minProb = 1e-04,
  yshift = -1,
  peakWidth = 0.5,
  textSize = 15
)

Arguments

isotope_numbers

A data.frame representing the isotope mass and abundance to be plotted.
charge

An integer representing the charge. Default is 1.
minProb

A numeric value representing the minimum probability. Default is 0.0001.
yshift

A numeric value representing the vertical shift applied to the plot for better visualization of the abundance close to 0. Default is -1.
peakWidth

A numeric value representing the width of the peaks in the plot. Default is 0.5.
textSize

A numeric value representing the size of the text in the plot.

Value

A ggplot object of molecular isotopes without fine structure by FFT algorithm

Examples

isotope_numbers <- cal_isotope_peaks_fft("C6H12O6", N_width = 200, min_abundance = 0.001, C13 = 0.5)
plotMolecularFFTisotopes(isotope_numbers)

Plot Molecular Isotopes with fine structure by Montecarlo algorithm

Description

This function generates a plot of molecular isotopes based on the provided isotope numbers.

Usage

plotMolecularIsotopes(
  isotope_numbers,
  charge = 1,
  minProb = 1e-04,
  jitterAmount = 0.03,
  yshift = -1,
  peakWidth = 0.5,
  labelN = 35,
  labelSize = 3,
  textSize = 15
)

Arguments

isotope_numbers

A data.frame representing the isotope mass and abundance to be plotted.
charge

An integer representing the charge of the molecule. Default is 1.
minProb

A numeric value representing the minimum probability threshold for plotting. Default is 0.0001.
jitterAmount

A numeric value representing the amount of jitter to be added to the plot for better visualization of adjacent MZ. Default is 0.03.
yshift

A numeric value representing the vertical shift applied to the plot for better visualization of the abundance close to 0. Default is -1.
peakWidth

A numeric value representing the isotopic peak width in the plot. Default is 0.5.
labelN

An integer setting top N peaks to be annotated. Default is 35.
labelSize

A numeric value representing the size of the isotopologues labels. Default is 3.
textSize

A numeric value representing the size of the text in the plot. Default is 15.

Value

ggplot A ggplot object of molecular isotopes generated by Montecarlo algorithm.

Examples

isotope_numbers <- cal_isotope_numbers_SIP("C6H12O6", num_simulations = 10000, C13 = 0.5)
plotMolecularIsotopes(isotope_numbers)

plot precursor annotation

Description

plot precursor annotation

Usage

plotPrecursorAnnotation(
  observedSpect,
  pep,
  charge,
  Atom,
  Prob,
  isoCenter = 0,
  isoWidth = 0,
  xwidth = 0,
  ifRemoveNotFoundIon = FALSE,
  ifShowPrecursorChargeAnnotation = TRUE,
  ifShowIsoCenter = TRUE,
  ifShowIsoWindow = TRUE,
  ifAdjustSIPabundance = TRUE,
  breakSize = 1/5,
  linewidth = 0.3
)

Arguments

observedSpect

AAspectra object of precursor scan
pep

peptide sequence
charge

precursor charge in consideration
Atom

SIP labeled atom "13C" or "15N" for exmaple
Prob

its SIP abundance (0.0~1.0)
isoCenter

isolation window center. Defaults to the center of observedSpect when 0.
isoWidth

isolation window width. Defaults to the m/z span of observedSpect when 0.
xwidth

x-axis display width around isoCenter. Defaults to the m/z span of the observed and expected peaks when 0.
ifRemoveNotFoundIon

set it FALSE as default
ifShowPrecursorChargeAnnotation

Logical. If TRUE, show precursor charge annotation labels with ggrepel. Default TRUE.
ifShowIsoCenter

Logical. If TRUE, show isoCenter as a black dashed vertical reference line. Default TRUE.
ifShowIsoWindow

Logical. If TRUE, show grey dashed vertical lines at isolation window boundaries (⁠isoCenter ± isoWidth/2⁠). Default TRUE.
ifAdjustSIPabundance

Logical. If TRUE, estimate and re-fit SIP abundance from initial precursor annotation. Default TRUE.
breakSize

Numeric multiplier for isolation window to compute x-axis break step. Default is 1/5.
linewidth

Numeric width of peaks. Default 0.3.

Value

ggplot2 layer

Examples

realMZ <- c(
  894.9413, 895.4429, 895.9444, 896.3896, 896.4448, 896.9463,
  897.3890, 897.8896, 898.3930, 898.4734, 901.8851, 902.4465,
  902.9483, 903.4498, 903.9504, 910.8968, 911.4449, 912.3784
)
realIntensity <- c(
  16660537.0, 12344664.0, 6128400.5, 1448961.1, 1614148.1, 713238.8,
  1999402.4, 1124157.4, 567865.2, 647140.8, 709644.2, 7805729.0,
  8421993.0, 3200114.2, 1286055.5, 620246.8, 540861.6, 1079918.5
)
realCharge <- c(2, 2, 2, 0, 2, 2, 2, 2, 2, 0, 0, 2, 2, 2, 2, 0, 0, 2)
scan <- list(
  peaks = data.frame(
    mz = realMZ,
    intensity = realIntensity,
    charge = realCharge
  ),
  precursorCharges = 2
)
observedSP <- getRealScanFromList(scan)
p <- plotPrecursorAnnotation(
  observedSpect = observedSP,
  pep = "GITINTSHVEYDTPTR", charge = 2,
  Atom = "C13", Prob = 0.01,
  isoCenter = 902.4471, isoWidth = 5.0, xwidth = 20.0,
  ifRemoveNotFoundIon = TRUE
)
p

Plot precursor MZ frequency per 5 per minute of MS2

Description

Plot precursor MZ frequency per 5 per minute of MS2

Usage

plotPrecursorMzFrequency(
  info,
  timeBinWidth = 1,
  x_breaks = seq(0, 200, by = 10)
)

Arguments

info

A data.frame of retention time and precursor mass
timeBinWidth

A numeric value of retention time bin width. Default is 1
x_breaks

A numeric vector of breaks for x axis. Default is seq(0, 200, by = 10)

Value

A ggplot layer of scan frequency of MS2

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
a <- getRetentionTimeAndPrecursorInfo(a)
plotPrecursorMzFrequency(a, timeBinWidth = 0.1, x_breaks = seq(8, 11, by = 0.2))

plot the distribution of SIP percent of proteins

Description

plot the distribution of SIP percent of proteins

Usage

plotProSipPct(proPath)

Arguments

proPath

a pro.cluster.txt file's path

Value

a ggplot2 obj

Examples

demo_file <- system.file("extdata", "demo.pro.cluster.txt", package = "Aerith")
p <- plotProSipPct(demo_file)
p

plot PSM annotation

Description

plot PSM annotation

Usage

plotPSMannotation(
  observedSpect,
  pep,
  Atom,
  Prob,
  charges,
  isoCenter = 0,
  isoWidth = 0,
  ifRemoveNotFoundIon = FALSE
)

Arguments

observedSpect

AAspectra object of real scan
pep

peptide sequence
Atom

SIP labeled atom "13C" or "15N" for exmaple
Prob

its SIP abundance (0.0~1.0)
charges

charges numeric vector for B/Y ions in consideration
isoCenter

isolation window center, set it 0 as default if not remove peaks in isolation window
isoWidth

isolation window width, set it 0 as default if not remove peaks in isolation window
ifRemoveNotFoundIon

set it False as default

Value

ggplot2 layer

Examples

demo_file <- system.file("extdata", "107728.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
a <- getRealScan("107728", a)
p <- plotPSMannotation(
    observedSpect = a,
    pep = "HSQVFSTAEDNQSAVTIHVLQGER", Atom = "C13", Prob = 0.01,
    charges = c(2), isoCenter = 886.65, isoWidth = 4.0,
    ifRemoveNotFoundIon = TRUE
)
p

plot PSMs from FT2 files and PSM results

Description

plot PSMs from FT2 files and PSM results

Usage

plotPSMs(
  realScans,
  charges,
  Atom = "C13",
  Probs,
  BYcharge = c(1, 2),
  ftFileNames,
  scanNumbers,
  pepSeqs,
  proNames,
  path = "."
)

Arguments

realScans

List of AAspectra objects of real scan
charges

Integer vector of precursor charge of PSMs
Atom

"C13" or "N15". Default is "C13"
Probs

C13 or N15's abundance of PSMs
BYcharge

Integer vector of B Y ion. Default is 1:2
ftFileNames

Character vector of FT2 file names
scanNumbers

Integer vector of scan number of PSMs
pepSeqs

Character vector of peptide sequence of PSMs
proNames

Character vector of protein name of PSMs
path

Output path of pdf. Default is "."

Value

PDF files saved in the specified path

Examples

element <- "C13"
demo_file <- system.file("extdata", "demo.psm.txt", package = "Aerith")
psm <- readPSMtsv(demo_file)
psm <- psm[psm$Filename == "Pan_052322_X13.FT2", ]
psm <- psm[psm$ScanNumber %in% c("4068", "2596", "8182"), ]
demo_file <- system.file("extdata", "X13_4068_2596_8182.FT2", package = "Aerith")
ft2 <- readAllScanMS2(demo_file)
ftFileNames <- psm$Filename
scanNumbers <- psm$ScanNumber
proNames <- psm$ProteinNames
charges <- psm$ParentCharge
pep <- psm$OriginalPeptide
pep <- stringr::str_sub(pep, 2, -2)
pct <- psm$SearchName
pct <- as.numeric(stringr::str_sub(
    stringr::str_split(pct, "_", simplify = TRUE)[, 2], 1, -4
)) / 100 / 1000
realScans <- getRealScans(ft2, scanNumbers)
tmp <- tempdir()
plotPSMs(
    realScans,
    charges,
    element,
    pct,
    BYcharge = 1:2,
    ftFileNames,
    scanNumbers,
    pep,
    proNames,
    path = tmp
)
list.files(tmp, pattern = ".pdf", full.names = TRUE)

Plot the distribution of SIP percent for PSMs

Description

This function reads a PSM file, processes the SIP percent values, and generates a histogram with a dashed vertical line indicating the median.

Usage

plotPSMsipPCT(psmPath)

Arguments

psmPath

A character string specifying the path to the PSM file.

Value

A ggplot2 object representing the histogram of SIP percent values.

Examples

demo_file <- system.file("extdata", "demo.psm.txt", package = "Aerith")
p <- plotPSMsipPCT(demo_file)
p

plot real scan layer under the B Y ion peaks

Description

plot real scan layer under the B Y ion peaks

Usage

plotRealScan(spect, linewidth = 0.1)

Arguments

spect

AAspectra object of real scan
linewidth

Value

ggplot2 layer

Examples

a <- getSipBYionSpectra("HSQVFSTAEDNQSAVTIHVLQGER", "C13", 0.01, 1:2)
p <- plot(a)
p <- p + plotSipBYionLabel(a)
demo_file <- system.file("extdata", "107728.FT2", package = "Aerith")
b <- readAllScanMS2(demo_file)
c <- getRealScan(107728, b)
p <- p + plotRealScan(c)
p

Plot scan frequency

Description

Plot scan frequency

Usage

plotScanFrequency(info, binwidth = 1, breaks = seq(0, 200, by = 10))

Arguments

info

A data.frame of retention time and precursor mass
binwidth

A numeric value of bin width. Default is 1
breaks

A numeric vector of breaks for x axis. Default is seq(0, 200, by = 10)

Value

A ggplot of scan frequency per minute

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getRetentionTimeAndPrecursorInfo(a)
plotScanFrequency(b, binwidth = 0.1, breaks = seq(9, 10, by = 0.2))
rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
a <- readAllScanMS1(demo_file)
b <- getRetentionTimeAndPrecursorInfo(a)
plotScanFrequency(b, binwidth = 0.1, breaks = seq(9, 10, by = 0.2))

Plot scan frequency layer of MS2

Description

Plot scan frequency layer of MS2

Usage

plotScanFrequencyMS2(info, binwidth = 1)

Arguments

info

A data.frame of retention time and precursor mass
binwidth

A numeric value of bin width. Default is 1

Value

A ggplot layer of scan frequency of MS2

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
a <- getRetentionTimeAndPrecursorInfo(a)
rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
b <- readAllScanMS1(demo_file)
b <- getRetentionTimeAndPrecursorInfo(b)
plotScanFrequency(a, binwidth = 0.1, breaks = seq(9, 10, by = 0.2)) + plotScanFrequencyMS2(b, binwidth = 0.1)

plot the score of PSMs at different charge and mass error

Description

plot the score of PSMs at different charge and mass error

Usage

plotScoreDistribution(sipFile)

Arguments

sipFile

a .sip file's path

Value

a ggplot2 obj

Examples

sipFile <- system.file("extdata", "demo.sip", package = "Aerith")
plotScoreDistribution(sipFile)

Draw AAspectra MS plot with B Y ion Labels

Description

Draw AAspectra MS plot with B Y ion Labels

Usage

plotSipBYionLabel(spect)

Arguments

spect

AAspectra object of B Y ions

Value

ggplot2 layer

Examples

a <- getSipBYionSpectra("KHRIPCDRK", "C13", 0.05, 1:2)
p <- plot(a)
p + plotSipBYionLabel(a)

Plot SIP-filtered PCT and intensity summary by each input file

Description

This function reads a SIP filtered PSM file, processes the data, and generates a hexbin plot of log2 precursor intensity vs. MS1 isotopic abundances, faceted by each input file.

Usage

plotSIPfilteredPCTIntensityBySample(
  psm_file = "SIP_filtered_psms.tsv",
  output_file = "SIP_filtered_PCT_and_intensity_summary_by_sample.pdf",
  width = 16,
  height = 12
)

Arguments

psm_file

Path to the filtered PSM file (e.g., "SIP_filtered_psms.tsv").
output_file

Output PDF file name for the plot.
width

Width of the output PDF (default: 16).
height

Height of the output PDF (default: 12).

Value

A ggplot2 object representing the hexbin plot.

Plot TIC of MS1 or MS2

Description

Plot TIC of MS1 or MS2

Usage

plotTIC(tic, breaks = seq(0, 200, by = 10))

Arguments

tic

A data.frame of TIC and retention time
breaks

A vector of breaks for x axis

Value

a ggplot2 object

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
a <- readAllScanMS2(demo_file)
b <- getTIC(a)
plotTIC(b, seq(9, 10, by = 0.2))

Precursor Peak Calculator

Description

This function calculates the isotopic distribution of a given amino acid string and returns a DataFrame containing the mass and probability of each isotope.

Usage

precursor_peak_calculator(AAstr)

Arguments

AAstr

A string representing the amino acid sequence.

Value

A DataFrame with two columns: "Mass" containing the mass of each isotope and "Prob" containing the probability of each isotope.

Examples

a <- precursor_peak_calculator("PEPTIDE")

Precursor Peak Calculator with User-Defined Isotopic Distribution

Description

This function calculates the isotopic distribution of a given amino acid string with a user-defined isotopic distribution and returns a DataFrame containing the mass and probability of each isotope.

Usage

precursor_peak_calculator_DIY(AAstr, Atom, Prob)

Arguments

AAstr

A string representing the amino acid sequence.
Atom

A string representing the isotope ("C13", "N15", "H2", "O18", "S34").
Prob

A double representing the abundance of the specified isotope (0.0 to 1.0).

Value

A DataFrame with two columns: "Mass" containing the mass of each isotope and "Prob" containing the probability of each isotope.

Examples

# Example usage
df <- precursor_peak_calculator_DIY("PEPTIDE", "C13", 0.2)
df <- precursor_peak_calculator_DIY("PEPTIDE", "N15", 0.5)

Simple peak calculator of user defined isotopic distribution of one peptide by averagine

Description

Simple peak calculator of user defined isotopic distribution of one peptide by averagine

Usage

precursor_peak_calculator_DIY_averagine(AAstrs, Atom, Prob)

Arguments

AAstrs

a CharacterVector of peptides
Atom

a CharacterVector C13 or N15
Prob

a NumericVector for its abundance

Value

a list of DataFrames of spectra

Examples

demoSpectra <- precursor_peak_calculator_DIY_averagine(c("PEPTIDE", "ACDEFGHIK"), "C13", 0.25)
demoSpectra[[1]]

rankify numeric vector via ftFileWriter

Description

rankify numeric vector via ftFileWriter

Usage

rankyfify(a)

Arguments

a

A numeric vector whose values will be rank-transformed.

Value

A numeric vector containing the ranks of the input values.

Examples

demo_vec <- c(12.5, 3.2, 7.7, 3.2)
rankyfify(demo_vec)

read MS1 scans with scanNumber as index

Description

read MS1 scans with scanNumber as index

Usage

readAllScanMS1(ftFile)

Arguments

ftFile

a ft1 file's full path

Value

a list of MS1 scans with names of scan number

Examples

rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
ft1 <- readAllScanMS1(demo_file)

read MS2 scans with scanNumber as index

Description

read MS2 scans with scanNumber as index

Usage

readAllScanMS2(ftFile)

Arguments

ftFile

a ft2 file's full path

Value

a list of MS2 scans with names of scan number

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
ft2 <- readAllScanMS2(demo_file)

readFilesScansTopPSMs

Description

Aggregate the top-ranked peptide-spectrum matches (PSMs) from each scan across all .sip files found in a directory.

Usage

readFilesScansTopPSMs(workingPath, topN)

Arguments

workingPath

Character vector of length one giving the directory that contains .sip files.
topN

Integer specifying how many top-ranked PSMs per scan to retain for each .sip file.

Details

This helper constructs an internal sipFileReader, loads every .sip file located in the supplied path, and extracts the best topN PSMs per scan. The result is returned as a single data.frame with file identifiers, scan numbers, charge states, mass measurements, scores, peptide assignments, and protein annotations.

Value

An R data.frame with one row per retained PSM and the columns fileNames, scanNumbers, parentCharges, measuredParentMasses, calculatedParentMasses, searchNames, scores, identifiedPeptides, originalPeptides, and proteinNames.

Examples

demo_dir <- system.file("extdata", package = "Aerith")
re <- readFilesScansTopPSMs(demo_dir, 10)
head(re)

readFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .sip files of one .FT2 file

Description

readFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .sip files of one .FT2 file

Usage

readFilesScansTopPSMsFromOneFT2(workingPath, pattern, topN)

Arguments

workingPath

a full path with .sip files in it
pattern

a regex pattern of the .FT2 file
topN

store top N PSMs of each scan of one .FT2 file

Value

a dataframe of top N PSMs

Examples

demo_dir <- system.file("extdata", package = "Aerith")
re <- readFilesScansTopPSMsFromOneFT2(demo_dir, ".*demo.*", 3)
head(re)

read FT file header

Description

read FT file header

Usage

readFTheader(ftFile)

Arguments

ftFile

a ft1 file's full path

Value

a list of ft file header

Examples

rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
header <- readFTheader(demo_file)

Read spectra from .mgf file

Description

Read spectra from .mgf file

Usage

readMgf(mgf)

Arguments

mgf

A .mgf file's path

Value

A list of spectra with names of scan number

Examples

demo_file <- system.file("extdata", "demo.mgf", package = "Aerith")
a <- readMgf(demo_file)
scan <- getRealScanFromList(a[["2648"]])
plot(scan)

Read MS1 spectra from .mzML file

Description

Read MS1 spectra from .mzML file

Usage

readMzmlMS1(ms)

Arguments

ms

A .mzML files's path

Value

A list of MS1 scans with names of scan number

Examples

# mzR can be installed from bioconductor
# library(mzR)
demo_file <- system.file("extdata", "demo.mzML", package = "Aerith")
a <- readMzmlMS1(demo_file)

Read MS2 spectra from .mzML file

Description

Read MS2 spectra from .mzML file

Usage

readMzmlMS2(ms)

Arguments

ms

A .mzML files's path

Value

A list of MS2 scans with names of scan number

Examples

# mzR can be installed from bioconductor
# library(mzR)
demo_file <- system.file("extdata", "demo.mzML", package = "Aerith")
a <- readMzmlMS2(demo_file)

readOneScanMS1

Description

readOneScanMS1

Usage

readOneScanMS1(ftFile, scanNumber)

Arguments

ftFile

a ft1 file's full path
scanNumber

the scan at scanNumber

Value

a list of MS1 scan

Examples

rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
ft1 <- readOneScanMS1(demo_file, 1588)

readOneScanMS2

Description

readOneScanMS2

Usage

readOneScanMS2(ftFile, scanNumber)

Arguments

ftFile

a ft2 file's full path
scanNumber

the scan at scanNumber

Value

a list of MS2 scan

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
ft2 <- readOneScanMS2(demo_file, 1633)

Read PSM table from .pepXML file

Description

Read PSM table from .pepXML file

Usage

readPepXMLtable(pepXML)

Arguments

pepXML

A .pepXML files's path

Value

A dataframe of psm table

Examples

# mzR can be installed from bioconductor
# library(mzR)
demo_file <- system.file("extdata", "demo.pepXML", package = "Aerith")
a <- readPepXMLtable(demo_file)

Read PSM TSV File

Description

This function reads a Peptide-Spectrum Match (PSM) file in TSV (Tab-Separated Values) format.

Usage

readPSMtsv(tsv)

Arguments

tsv

A character string specifying the path to the PSM TSV file.

Value

A data frame containing the data from the PSM TSV file.

Examples

demo_file <- system.file("extdata", "demo.psm.txt", package = "Aerith")
a <- readPSMtsv(demo_file)

read MS1 scans with scanNumber as index in a range

Description

read MS1 scans with scanNumber as index in a range

Usage

readScansMS1(ftFile, startScanNumber, endScanNumber)

Arguments

ftFile

a ft1 file's full path
startScanNumber

read scans starting from this scanNumber
endScanNumber

read scans ending at this scanNumber

Value

a list of MS1 scans with names of scan number

Examples

rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
ft1 <- readScansMS1(demo_file, 1398, 1503)

read MS1 scans with scanNumber as index in a vector

Description

read MS1 scans with scanNumber as index in a vector

Usage

readScansMS1Vector(ftFile, scanNumbersVector)

Arguments

ftFile

a ft1 file's full path
scanNumbersVector

a NumericVector of scan numbers

Value

A named list of MS1 scans with names of scan number. The names of the list correspond to the scan numbers.

Examples

rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
ft1 <- readScansMS1Vector(demo_file, c(1398, 1503, 1508))

read MS2 scans with scanNumber as index in a range

Description

read MS2 scans with scanNumber as index in a range

Usage

readScansMS2(ftFile, startScanNumber, endScanNumber)

Arguments

ftFile

a ft2 file's full path
startScanNumber

read scans starting from this scanNumber
endScanNumber

read scans ending at this scanNumber

Value

a list of MS2 scans with names of scan number

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
ft2 <- readScansMS2(demo_file, 1350, 1355)

read MS2 scans with scanNumber as index in a vector

Description

read MS2 scans with scanNumber as index in a vector

Usage

readScansMS2Vector(ftFile, scanNumbersVector)

Arguments

ftFile

a ft2 file's full path
scanNumbersVector

read scans starting of these scanNumbers

Value

a list of MS2 scans with names of scan number

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
ft2 <- readScansMS2Vector(demo_file, c(1350, 1355, 1359))

readSip

Description

Read a single .sip file and convert its peptide-spectrum matches (PSMs) into an R list.

Usage

readSip(sipFile)

Arguments

sipFile

A character vector of length one containing the full path to a .sip file.

Details

The reader parses the provided .sip file and returns metadata together with a data.frame of PSM-level attributes.

Value

An R list with file-level metadata (fileName, scanType, searchName, scoringFunction) and a PSM data frame containing scan numbers, charges, masses, scores, ranks, peptides, and protein names.

Examples

demo_file <- system.file("extdata", "demo.sip", package = "Aerith")
re <- readSip(demo_file)
head(re$PSM)

readSips

Description

Read every .sip file found in the provided directory and transform each file's peptide-spectrum matches into an R list entry.

Usage

readSips(workingPath)

Arguments

workingPath

Character vector of length one giving the directory that contains .sip files.

Details

This function constructs a sipFileReader for the supplied folder, loads all .sip files, and for each file returns a list containing metadata and a data.frame of peptide-spectrum matches (PSMs). The resulting object is an R list whose elements correspond to individual input files.

Value

An R list; each element represents one .sip file and provides file-level descriptors (fileName, scanType, searchName, scoringFunction) together with a PSM data frame holding scan numbers, precursor charges, observed/calculated masses, scores, ranks, peptide sequences, and protein assignments.

Examples

demo_dir <- system.file("extdata", package = "Aerith")
re <- readSips(demo_dir)
head(re[[1]]$PSM)

readSpe2Pep

Description

readSpe2Pep

Usage

readSpe2Pep(Spe2PepFile)

Arguments

Spe2PepFile

a .Spe2PepFile file's full path

Value

the PSMs in a dataframe in a list

Examples

target_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
psm <- readSpe2Pep(target_file)
psm <- psm$PSM

readSpe2PepFilesScansTopPSMs read each scan's top PSMs from multiple .Spe2Pep.txt files

Description

readSpe2PepFilesScansTopPSMs read each scan's top PSMs from multiple .Spe2Pep.txt files

Usage

readSpe2PepFilesScansTopPSMs(workingPath, topN = 5L)

Arguments

workingPath

a full path with .Spe2Pep.txt files in it
topN

store top N PSMs of each scan of one .FT2 file

Value

the PSMs in a dataframe in a list

Examples

tmp <- tempdir()
sip_dir <- file.path(tmp, "sip")
dir.create(sip_dir)
demo_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000target.Spe2Pep.txt"))
demo_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000decoy.Spe2Pep.txt"))
list.files(sip_dir, full.names = TRUE)
psm <- readSpe2PepFilesScansTopPSMs(sip_dir, 3)

readSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file

Description

readSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file

Usage

readSpe2PepFilesScansTopPSMsFromEachFT2Parallel(workingPath, topN = 5L)

Arguments

workingPath

a full path with .Spe2PepFile.txt files in it
topN

store top N PSMs of each scan of one .FT2 file

Value

a dataframe of top N PSMs

Examples

tmp <- tempdir()
sip_dir <- file.path(tmp, "sip")
dir.create(sip_dir)
demo_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000target.Spe2Pep.txt"))
demo_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000decoy.Spe2Pep.txt"))
list.files(sip_dir, full.names = TRUE)
top3 <-  readSpe2PepFilesScansTopPSMsFromEachFT2Parallel(sip_dir, 3)

readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParalle read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file

Description

readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParalle read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file

Usage

readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel(
  targetPath,
  decoyPath,
  topN = 5L
)

Arguments

targetPath

a full path with target .Spe2PepFile.txt files in it
decoyPath

a full path with decoy .Spe2PepFile.txt files in it
topN

store top N PSMs of each scan of one .FT2 file

Value

a dataframe of top N PSMs

Examples

tmp <- tempdir()
target_dir <- file.path(tmp, "target")
dir.create(target_dir, showWarnings = FALSE)
target_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(target_file, file.path(target_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
decoy_dir <- file.path(tmp, "decoy")
dir.create(decoy_dir, showWarnings = FALSE)
decoy_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(decoy_file, file.path(decoy_dir, "Pan_052322_X13.SIP_C13_050_000Pct.Spe2Pep.txt"))
list.files(target_dir, full.names = TRUE)
list.files(decoy_dir, full.names = TRUE)
top3 <- readSpe2PepFilesScansTopPSMsFromEachFT2TargetAndDecoyParallel(target_dir, decoy_dir, 3)

readSpe2PepFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .Spe2PepFile.txt files of one .FT2 file

Description

readSpe2PepFilesScansTopPSMsFromOneFT2 read each scan's top PSMs from multiple .Spe2PepFile.txt files of one .FT2 file

Usage

readSpe2PepFilesScansTopPSMsFromOneFT2(workingPath, pattern, topN = 5L)

Arguments

workingPath

a full path with .Spe2PepFile.txt files in it
pattern

a regex pattern of the .FT2 file
topN

store top N PSMs of each scan of one .FT2 file

Value

a dataframe of top N PSMs

Examples

tmp <- tempdir()
sip_dir <- file.path(tmp, "sip")
dir.create(sip_dir)
demo_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000target.Spe2Pep.txt"))
demo_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000decoy.Spe2Pep.txt"))
list.files(sip_dir, full.names = TRUE)
top3 <-  readSpe2PepFilesScansTopPSMsFromOneFT2(sip_dir, ".*X13.*", 3)

readSpe2Peps

Description

readSpe2Peps

Usage

readSpe2Peps(workingPath)

Arguments

workingPath

a full path with .Spe2Pep.txt files in it

Value

the PSMs dataframes in lists

Examples

tmp <- tempdir()
sip_dir <- file.path(tmp, "sip")
dir.create(sip_dir)
demo_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000target.Spe2Pep.txt"))
demo_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000decoy.Spe2Pep.txt"))
list.files(sip_dir, full.names = TRUE)
psm <- readSpe2Peps(sip_dir)
psm <- psm[[1]]$PSM

Simple residue peak calculator of user defined isotopic distribution of one residue

Description

Simple residue peak calculator of user defined isotopic distribution of one residue

Usage

residue_peak_calculator_DIY(residue, Atom, Prob)

Arguments

residue

residue name
Atom

isotopes of "C13", "N15", "H2", "O18", "S34"
Prob

its SIP abundance (0.0~1.0)

Value

A DataFrame with two columns: "Mass" containing the mass of each isotope and "Prob" containing the probability of each isotope.

Examples

df <- residue_peak_calculator_DIY("A", "C13", 0.2)

scoreIntensity

Description

scoreIntensity

Usage

scoreIntensity(observed, realIntensity, expectedIntensity, Atom, Prob)

Arguments

observed

this peak is observed or not
realIntensity

real intensity in MS2 scan
expectedIntensity

expected intensity
Atom

"C13" or "N15"
Prob

its SIP abundance (0.0~1.0)

Value

a score of this intensity match

Examples

scoreIntensity(TRUE, 1200.0, 1180.0, "C13", 0.02)

scoreIntensityByCrossEntropy

Description

scoreIntensityByCrossEntropy

Usage

scoreIntensityByCE(expectedIntensity, observedIntensity)

Arguments

expectedIntensity

expected intensityreal
observedIntensity

observed intensity in MS2 scan

Value

numeric, a score of this intensity match

Examples

scoreIntensityByCE(c(10.0, 20.0, 30.0), c(9.5, 21.0, 28.0))

scorePSM

Description

scorePSM

Usage

scorePSM(realMZ, realIntensity, realCharge, parentCharge, pepSeq, Atom, Prob)

Arguments

realMZ

mz vector in MS2 scan
realIntensity

intensity vector in MS2 scan
realCharge

charge vector in MS2 scan
parentCharge

int parent charge of MS2 scan
pepSeq

a string of peptide
Atom

"C13" or "N15"
Prob

its SIP abundance (0.0~1.0)

Value

a score of this PSM

Examples

demo_file <- system.file("extdata", "107728.FT2", package = "Aerith")
scan1 <- readOneScanMS2(ftFile = demo_file, 107728)
score <- scorePSM(scan1$peaks$mz,
        scan1$peaks$intensity, scan1$peaks$charge, 2,
        "[HSQVFSTAEDNQSAVTIHVLQGER]", "C13", 0.0107)

scorePSMsimple Score a PSM without isotopic envelope shape modeling

Description

scorePSMsimple Score a PSM without isotopic envelope shape modeling

Usage

scorePSMsimple(
  realMZ,
  realIntensity,
  realCharge,
  parentCharge,
  pepSeq,
  Atom,
  Prob
)

Arguments

realMZ

mz vector in MS2 scan
realIntensity

intensity vector in MS2 scan
realCharge

charge vector in MS2 scan
parentCharge

precursor charge, 2 for example
pepSeq

a string of peptide
Atom

"C13" or "N15"
Prob

its SIP abundance (0.0~1.0)

Value

a score of this PSM

Examples

demo_file <- system.file("extdata", "107728.FT2", package = "Aerith")
scan1 <- readOneScanMS2(ftFile = demo_file, scanNumber = 107728)
score <- scorePSMsimple(
  scan1$peaks$mz,
  scan1$peaks$intensity,
  scan1$peaks$charge,
  2,
  "[HSQVFSTAEDNQSAVTIHVLQGER]",
  "C13",
  0.0107
)

Summarize SIP percent for PSMs

Description

This function reads a PSM file and computes summary statistics for the SIP percent values, including the total count, average, median, Median Absolute Deviation (MAD), standard deviation, estimated FDR, the number of labeled PSMs, and the median SIP percent for the labeled PSMs.

Usage

summaryPSMsipPCT(psmPath, SIPthreshold = 5, chargeThreshold = 3)

Arguments

psmPath

A character string specifying the path to the PSM file.
SIPthreshold

Numeric value representing the SIP threshold (default is 5).
chargeThreshold

Numeric value representing the parent charge threshold (default is 3).

Value

A data frame containing summary statistics of the SIP percent values.

Examples

demo_file <- system.file("extdata", "demo.psm.txt", package = "Aerith")
summaryStats <- summaryPSMsipPCT(demo_file)
print(summaryStats)

write all MS1 scans has charge

Description

write all MS1 scans has charge

Usage

writeAllScanMS1(header, scansList, ftFile)

Arguments

header

a list of FT file header
scansList

a list of scans for output
ftFile

a ft1 file's output path

Value

TRUE if the file was written successfully, FALSE otherwise

Examples

rds <- system.file("extdata", "demo.FT1.rds", package = "Aerith")
demo_file <- tempfile(fileext = ".FT1")
writeLines(readRDS(rds), demo_file)
header <- readFTheader(demo_file)
ft1 <- readAllScanMS1(demo_file)
tmp <- tempdir()
writeAllScanMS1(header, ft1[1:10], file.path(tmp, "demo10.FT1"))
list.files(tmp, pattern = "demo10.FT1", full.names = TRUE)

write all MS2 scans has charge

Description

write all MS2 scans has charge

Usage

writeAllScanMS2(header, scansList, ftFile)

Arguments

header

a list of FT file header
scansList

a list of scans for output
ftFile

a ft2 file's output path

Value

TRUE if the file was written successfully, FALSE otherwise

Examples

demo_file <- system.file("extdata", "demo.FT2", package = "Aerith")
header <- readFTheader(demo_file)
ft2 <- readAllScanMS2(demo_file)
tmp <- tempdir()
writeAllScanMS2(header,ft2[1:10],file.path(tmp, "demo10.FT2"))
list.files(tmp, pattern = "demo10.FT2", full.names = TRUE)

writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file and write them to one tsv file

Description

writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel read each scan's top PSMs from multiple .Spe2PepFile.txt files of each .FT2 file and write them to one tsv file

Usage

writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel(
  workingPath,
  topN = 5L,
  fileName = "a.tsv"
)

Arguments

workingPath

a full path with .Spe2PepFile.txt files in it
topN

store top N PSMs of each scan of one .FT2 file
fileName

the output path

Value

nothing but write a tsv of top N PSMs

Examples

tmp <- tempdir()
sip_dir <- file.path(tmp, "sip")
dir.create(sip_dir)
demo_file <- system.file("extdata", "demo_target.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000target.Spe2Pep.txt"))
demo_file <- system.file("extdata", "demo_decoy.Spe2Pep.txt", package = "Aerith")
file.copy(demo_file, file.path(sip_dir, "Pan_052322_X13.SIP_C13_050_000decoy.Spe2Pep.txt"))
writeSpe2PepFilesScansTopPSMsFromEachFT2Parallel(sip_dir, 3, file.path(sip_dir, "top3.tsv"))
list.files(sip_dir, full.names = TRUE)
print(file.info(file.path(sip_dir, "top3.tsv")))