Package 'specL' reference manual

Title:	specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Description:	provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>.
Authors:	Christian Panse [aut, cre] , Jonas Grossmann [aut] , Christian Trachsel [aut], Witold E. Wolski [ctb]
Maintainer:	Christian Panse <[email protected]>
License:	GPL-3
Version:	1.41.0
Built:	2024-10-31 05:25:43 UTC
Source:	https://github.com/bioc/specL

Annotate protein_id

Description

This function assigns the protein identifier for a list of tandem mass specs having a peptide sequence assigned.

Usage


annotate.protein_id(data, file = NULL, fasta = read.fasta(file = file, 
         as.string = TRUE, seqtype = "AA"), digestPattern = "(([RK])|(^)|(^M))") 

annotate.protein_id(data, file = NULL, fasta = read.fasta(file = file, 
         as.string = TRUE, seqtype = "AA"), digestPattern = "(([RK])|(^)|(^M))")

Arguments

`data`	list of records containing mZ and peptide sequences.
`file`	file name of a FASTA file.
`fasta`	a fasta object as returned by the `seqinr::read.fasta(...)` method.
`digestPattern`	a regex pattern which can be used by the `grep` command. the default regex pattern assumes a tryptic digest.

Details

The protein sequences a read by the read.fasta function of the seqinr package. The protein identifier is written to the protein proteinInformation variable.

If the function is called on a multi-core architecture it uses mclapply.

It is recommended to load the FASTA file prior to running annotate.protein_id using

myFASTA <- read.fasta(file = file, as.string = TRUE, seqtype = "AA")

instead of providing the FASTA file name to the function.

Value

it returns a list object.

Author(s)

Jonas Grossmann and Christian Panse, 2014

Examples


    # annotate.protein_id
    
    # our Fasta sequence
      irtFASTAseq <- paste(">zz|ZZ_FGCZCont0260|", 
      "iRT_Protein_with_AAAAK_spacers concatenated Biognosys\n",
      "LGGNEQVTRAAAAKGAGSSEPVTGLDAKAAAAKVEATFGVDESNAKAAAAKYILAGVENS",
      "KAAAAKTPVISGGPYEYRAAAAKTPVITGAPYEYRAAAAKDGLDAASYYAPVRAAAAKAD",
      "VTPADFSEWSKAAAAKGTFIIDPGGVIRAAAAKGTFIIDPAAVIRAAAAKLFLQFGAQGS",
      "PFLK\n")
      
    # be realistic, do it from file
      Tfile <- file();  cat(irtFASTAseq, file = Tfile);
      
    #use read.fasta from seqinr
      fasta.irtFASTAseq <-read.fasta(Tfile, as.string=TRUE, seqtype="AA")
      close(Tfile)
    
    #annotate with proteinID 
    # -> here we find all psms from the one proteinID above
      peptideStd <- specL::annotate.protein_id(peptideStd, 
      fasta=fasta.irtFASTAseq)
  
    #show indices for all PSMs where we have a proteinInformation
     which(unlist(lapply(peptideStd, 
      function(x){nchar(x$proteinInformation)>0})))

# annotate.protein_id
    
    # our Fasta sequence
      irtFASTAseq <- paste(">zz|ZZ_FGCZCont0260|", 
      "iRT_Protein_with_AAAAK_spacers concatenated Biognosys\n",
      "LGGNEQVTRAAAAKGAGSSEPVTGLDAKAAAAKVEATFGVDESNAKAAAAKYILAGVENS",
      "KAAAAKTPVISGGPYEYRAAAAKTPVITGAPYEYRAAAAKDGLDAASYYAPVRAAAAKAD",
      "VTPADFSEWSKAAAAKGTFIIDPGGVIRAAAAKGTFIIDPAAVIRAAAAKLFLQFGAQGS",
      "PFLK\n")
      
    # be realistic, do it from file
      Tfile <- file();  cat(irtFASTAseq, file = Tfile);
      
    #use read.fasta from seqinr
      fasta.irtFASTAseq <-read.fasta(Tfile, as.string=TRUE, seqtype="AA")
      close(Tfile)
    
    #annotate with proteinID 
    # -> here we find all psms from the one proteinID above
      peptideStd <- specL::annotate.protein_id(peptideStd, 
      fasta=fasta.irtFASTAseq)
  
    #show indices for all PSMs where we have a proteinInformation
     which(unlist(lapply(peptideStd, 
      function(x){nchar(x$proteinInformation)>0})))

This function computes dynamic SWATH windows (cdsw) for a given vector of numeric values, an psmSet class, or an specLSet class. The input R data object can be generated using the read.bibliospec function.

Usage

    cdsw(x, n=20, overlap=1, ...)
cdsw(x, n=20, overlap=1, ...)

Arguments

`x`	Numeric vector or psmSet class.
`n`	Number of desired SWATH windows. Default is set to 20.
`overlap`	Overlap of SWATH windows. The default is 1 Dalton.
`...`	pass arguments to `hist` function.

Details

The function determines the SWATH windows using the quantile function.

Value

The output is data.frame having the attributes from, to, mid, width, and counts. In the ideal output all bins should contain the same number of numeric values. This requirement is violated because the window borders are rounded with no digit after the comma.

Author(s)

Christian Panse, Christian Trachsel, 2015, 2016

Examples


  # do not plot histogram
  cdsw(peptideStd, plot = FALSE,  overlap = 0)
  
  # plot hist
  cdsw(peptideStd, freq = TRUE)
  
  # pre-filtering
  ## cdsw(x=q1[350 <= q1 & q1 <= 1250], n=20, overlap = 0, freq=TRUE)
# do not plot histogram
  cdsw(peptideStd, plot = FALSE,  overlap = 0)
  
  # plot hist
  cdsw(peptideStd, freq = TRUE)
  
  # pre-filtering
  ## cdsw(x=q1[350 <= q1 & q1 <= 1250], n=20, overlap = 0, freq=TRUE)

Spectrum library generator for SWATH analysis

Description

This function generates an ion library for SWATH analysis. It takes a R data object which contains a peak list. The R data object can be generated using the read.bibliospec function.

Usage


    genSwathIonLib(data, 
        data.fit = data,
        mascotIonScoreCutOFF=20,
        proteinIDPattern='',
        max.mZ.Da.error = 0.1,
        ignoreMascotIonScore = TRUE,
        topN = 10,
        fragmentIonMzRange = c(300, 1800),
        fragmentIonRange = c(4, 100),
        fragmentIonFUN = .defaultSwathFragmentIon,
        iRT = specL::iRTpeptides,
        AminoAcids = protViz::AA,
        breaks=NULL,
        NORMALIZE=.normalize_rt)
genSwathIonLib(data, 
        data.fit = data,
        mascotIonScoreCutOFF=20,
        proteinIDPattern='',
        max.mZ.Da.error = 0.1,
        ignoreMascotIonScore = TRUE,
        topN = 10,
        fragmentIonMzRange = c(300, 1800),
        fragmentIonRange = c(4, 100),
        fragmentIonFUN = .defaultSwathFragmentIon,
        iRT = specL::iRTpeptides,
        AminoAcids = protViz::AA,
        breaks=NULL,
        NORMALIZE=.normalize_rt)

Arguments

`data`	data set containing mZ and peptide sequence.
`mascotIonScoreCutOFF`	a value for filtering the specs.
`proteinIDPattern`	a filter for protein.
`max.mZ.Da.error`	the mZ error in Dalton on ms2 level.
`ignoreMascotIonScore`	Boolean if mascot score is considered or not.
`topN`	returns the most `N` intense fragment ion only.
`fragmentIonMzRange`	mZ range filter of fragment ion.
`fragmentIonRange`	range filter of the number of identified fragment ion which are assigned in the spectrum library set in `fragmentIonTyp`. Use this option to generate a library with a minimum of five transitions for all peptides using `c(5,100)`, all peptides where at least not five transmissions found were omitted.
`fragmentIonFUN`	`function (b, y)` which derives all requested fragment ion out a given tuple of `b` and `y` ion. If the parameter is not specified the method uses an internal function similar as the example below.
`iRT`	optional table which contains iRT peptides. If an iRT table is provided (default) a `lm` is applied to normalize the rt in `data`. See also `?iRT`. A necessary condition is that `data` contains at least two iRT peptides.
`AminoAcids`	a list containing of 1-letter code and mono-isotopic mass of the amino acids. Default uses the `protViz::AA` data set.
`data.fit`	data set containing mZ and peptide sequence which is used for normalizing rt using a linear model `lm(formula = rt ~ aggregateInputRT * fileName, data)`. The rt aggregation for the model uses `median`.
`breaks`	provides a vector of SWATH windows. If q1 (precursor mass) and q3 (fragment ion) fall into the same SWATH window the fragment ion is ignored in the resulting ion library. The follwing code shows an example `breaks=seq(400, 2000, by=25)`.
`NORMALIZE`	is a `function(data, data.fit, iRT, plot=FALSE)` normalizing the rt. The default is a internal R helper function using `lm`.

Details

The function is the main contribution of the specL package. It generates the spectra library used in a SWATH analysis workflow out of a mass spectrometric measurement.

genSwathIonLib uses the core functions protViz::findNN, protViz::fragmentIon, and protViz::aa2mass.

The input is read by using read.bibliospec function of this package and passed by the data function parameter. If no BiblioSpec files are available also Mascot DAT files can be read using scripts contained in the protViz package exec folder.

If the protein information is lost you can benefit for the specL::annotate.protein_id.Rd method.

The function first appear in the protViz 0.1.45 package. It has been removed in protViz 0.2.6 to avoid package dependencies.

Value

The output is a data structure defined as specLSet object. The generic method ionlibrary returns a list of specL objects, specLSet also stores the input and normalized retention times.

Author(s)

Christian Panse, Christian Trachsel, and Jonas Grossmann 2012, 2013, 2014, 2016

Examples


    myFragmentIon <- function (b, y) {
        Hydrogen <- 1.007825
        Oxygen <- 15.994915
        Nitrogen <- 14.003074

        b1_ <- (b )
        y1_ <- (y ) 

        b2_ <- (b + Hydrogen) / 2
        y2_ <- (y + Hydrogen) / 2 

        b3_ <- (b + 2 * Hydrogen) / 3
        y3_ <- (y + 2 * Hydrogen) / 3

        return( cbind(b1_, y1_, b2_, y2_, b3_, y3_) )
    }

    peptideStd.ionLib <- genSwathIonLib(data=peptideStd, 
        data.fit=peptideStd.redundant, 
        fragmentIonFUN=myFragmentIon)
        
        
    summary(peptideStd.ionLib)


    idx<-40

    op <- par(mfrow = c(2,1))

    plot(peptideStd.ionLib)

    text(rt.input(peptideStd.ionLib)[idx],
        rt.normalized(peptideStd.ionLib)[idx],
        "X", cex=1.5)

    plot(ionlibrary(peptideStd.ionLib)[[idx]])


    ## Not run: 
        write.spectronaut(peptideStd.ionLib, 
            file="peptideStd.ionLib.csv")
   
## End(Not run)
myFragmentIon <- function (b, y) {
        Hydrogen <- 1.007825
        Oxygen <- 15.994915
        Nitrogen <- 14.003074

        b1_ <- (b )
        y1_ <- (y ) 

        b2_ <- (b + Hydrogen) / 2
        y2_ <- (y + Hydrogen) / 2 

        b3_ <- (b + 2 * Hydrogen) / 3
        y3_ <- (y + 2 * Hydrogen) / 3

        return( cbind(b1_, y1_, b2_, y2_, b3_, y3_) )
    }

    peptideStd.ionLib <- genSwathIonLib(data=peptideStd, 
        data.fit=peptideStd.redundant, 
        fragmentIonFUN=myFragmentIon)
        
        
    summary(peptideStd.ionLib)


    idx<-40

    op <- par(mfrow = c(2,1))

    plot(peptideStd.ionLib)

    text(rt.input(peptideStd.ionLib)[idx],
        rt.normalized(peptideStd.ionLib)[idx],
        "X", cex=1.5)

    plot(ionlibrary(peptideStd.ionLib)[[idx]])


    ## Not run: 
        write.spectronaut(peptideStd.ionLib, 
            file="peptideStd.ionLib.csv")
   
## End(Not run)

iRT peptides - independent retention time peptides

Description

iRTpeptides data are used for genSwathIonLib rt normalization assuming.

iRTpeptides first appear in the protViz 0.1.45 package. It has been removed in protViz 0.2.10 to avoid package dependencies.

Format

contains a table

Author(s)

Jonas Grossmann and Christian Panse 2013

References

Using iRT, a normalized retention time for more targeted measurement of peptides. Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O. Source Proteomics. 2012 Apr;12(8):1111-21. doi: 10.1002/pmic.201100463.

Examples


    plot(sort(iRTpeptides$rt))

    plot(pim<-protViz::parentIonMass(as.character(iRTpeptides$peptide)) ~ iRTpeptides$rt)

plot(sort(iRTpeptides$rt))

    plot(pim<-protViz::parentIonMass(as.character(iRTpeptides$peptide)) ~ iRTpeptides$rt)

ms1 mass

Description

ms1.p2069 contains 11830 peptide pre cursor m/z values of human proteins.

Format

contains a numeric vector

Author(s)

Christian Panse

Peptide standard

Description

This dataset is a list of a peptide spectrum matches (protein identification result) from two standard runs.

Format

contains a list of peptide spectrum assignments.

Details

These standard runs (LCMS experiments) are routinely run on well maintained instruments. In this case a standard run consits of a digest of the FETUIN_BOVINE protein (400 amol) and iRT peptides.

Author(s)

Christian Panse, Christian Trachsel and Jonas Grossmann 2014

Examples


    peakplot(peptideStd[[40]]$peptideSequence, peptideStd[[40]])

    ## Not run: 

        download.file("http://fgcz-data.uzh.ch/~cpanse/specL/data/peptideStd.blib", 
            destfile="peptideStd.blib")

        download.file("http://fgcz-data.uzh.ch/~cpanse/specL/data/peptideStd.redundant.blib", 
            destfile="peptideStd.redundant.blib")

        # checksum

        if (require(tools)){
            md5sum(c("peptideStd.blib", "peptideStd.redundant.blib")) == 
                c("3f231931e54efd6516d7aa302073b17f", 
                    "8bab829d9e99344136613a17c0374b90")
        }

        peptideStd <- read.bibliospec("peptideStd.blib")
        peptideStd.redundant <- read.bibliospec("peptideStd.redundant.blib")

    
## End(Not run)

peakplot(peptideStd[[40]]$peptideSequence, peptideStd[[40]])

    ## Not run: 

        download.file("http://fgcz-data.uzh.ch/~cpanse/specL/data/peptideStd.blib", 
            destfile="peptideStd.blib")

        download.file("http://fgcz-data.uzh.ch/~cpanse/specL/data/peptideStd.redundant.blib", 
            destfile="peptideStd.redundant.blib")

        # checksum

        if (require(tools)){
            md5sum(c("peptideStd.blib", "peptideStd.redundant.blib")) == 
                c("3f231931e54efd6516d7aa302073b17f", 
                    "8bab829d9e99344136613a17c0374b90")
        }

        peptideStd <- read.bibliospec("peptideStd.blib")
        peptideStd.redundant <- read.bibliospec("peptideStd.redundant.blib")

    
## End(Not run)

Method for Function `plot` in Package specL

Description

This methode has no additional arguments.

Value

The method plots on the current device.

Methods

signature(x = "specL"): Plots the specL determined ions.
signature(x = "specLSet"): Plots retention time versus retention time.

BiblioSpec Reader

Description

This function reads a BiblioSpec generated file and returns a list of tandem mass specs (psm objects), peptide assignments, retention times, and modifications records. The type of the data structire which is returned is called psmSet.

Usage


    read.bibliospec(file)
read.bibliospec(file)

Arguments

file

the name of the BiblioSpec generated SQLite file.

Details

The function performs a SQL query on the SQLite files generated by bibliospec using the RSQLite package. The function is required for generating spec libraries used in a SWATH workflow.

BiblioSpec files are generated by using Skyline.

Value

It returns a list which can be read by the genSwathIonLib function and the protViz::peakplot function.

Author(s)

Christian Panse, 2014, 2015

Examples


    read.bibliospec
read.bibliospec

Methods for Function `show` in Package specL ~~

Description

Methods for function show in package specL ~~ writes specL or specLSet objects to a file or console.

Methods

signature(x = "specL"): Prints specL object data to the console.
signature(x = "specLSet"): Prints specL object data to the console.

Class `"specL"`

Description

This class is used to store, print, and plot the generated results of the package.

Objects from the Class

Objects can be created by calls of the form new("specL", ...).

Slots

group_id:: Object of class "character" just an id
peptide_sequence:: Object of class "character" AA sequence
proteinInformation:: Object of class "character" a string contains the protein identifier.
q1:: Object of class "numeric" peptide weight m/Z as measured by the MS device
q1.in_silico:: Object of class "numeric" peptide weight m/Z computed in-silico.
q3:: Object of class "numeric" measured fragment ions.
q3.in_silico:: Object of class "numeric" in-silico derived fragment ions.
score:: Object of class "numeric" taken from bibliospec - psm score
prec_z:: Object of class "numeric" pre-cursor charge.
frg_type:: Object of class "character" fragmenbt ion type, e.g., b or y ion.
frg_nr:: Object of class "numeric" fragment ion number
frg_z:: Object of class "numeric" fragment ion charge.
relativeFragmentIntensity:: Object of class "numeric" percentage base peaks of frament ions.
irt:: Object of class "numeric" independent retention time in seconds.
peptideModSeq:: Object of class "numeric" a vector contains the mass diff between AA and mod AA.
mZ.error:: Object of class "numeric" a string contains the protein identifier.
filename:: Object of class "character" a string contains the filename of the ions.

Methods

plot: signature(x = "specL"): plots the fragment ions of specL object.
show: signature(x = "specL"): shows the content of specL object.
write.spectronaut: signature(x = "specL"): writes the specL object to a ASCII file.

Note

No notes yet.

Author(s)

Christian Panse 2014

Examples


    showClass("specL")

showClass("specL")

Class `"specLSet"`

Description

This class is used to store, show, and write generated results of the package.

Objects from the Class

Objects can be created by calls of the form new("specLSet", ...).

Slots

input.parameter:: A list of parameter values.
ionlibrary:: A list of "specL" objects.
rt.normalized:: A numeric vector of normalized retention time values.
rt.input:: A numeric vector of retention time values.

Methods

show: signature(x = "specLSet"): shows the object content.
summary: signature(x = "specLSet"): print summary of object content.
plot: signature(x = "specLSet"): plots normalized versus input rt.
write.spectronaut: signature(x = "specLSet"): writes object to ASCII file.
generate.consensus: signature(x = "specLSet"): generates consensus specLSet object by combining all specL objects having a redundant group_id which is defined by paste([email protected]_silico, x@peptideModSeq, sep='_').
merge.specLSet: signature(x = "specLSet"): merges two specLSet objects.
ionlibrary: signature(x = "specLSet"): returns a list of specL objects.
rt.input: signature(x = "specLSet"): returns a numeric vector of input rt values.
rt.normalized: signature(x = "specLSet"): returns a numeric vector of normalized rt values.
getProteinPeptideTable: signature(x = "specLSet"): returns table of peptide protein mappings.

Note

No notes yet.

Author(s)

Christian Panse 2014

Examples


    showClass("specL")
    showClass("specLSet")

showClass("specL")
    showClass("specLSet")

Methods for Function `write.spectronaut` in Package specL

Description

Methods for function write.spectronaut in package specL ~~ writes specL objects to a file in a format which can be read by the 'Spectronaut' software. additional arguments are

file: A file name. default is file='spec.txt'.

Methods

signature(x = "specL"): Prints specL object data to to a file.
signature(x = "specLSet"): Prints specL object data to to a file.

Package 'specL'

Help Index

Annotate protein_id

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Generate Dynamic SWATH Window

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Spectrum library generator for SWATH analysis

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

iRT peptides - independent retention time peptides

Description

Format

Author(s)

References

Examples

ms1 mass

Description

Format

Author(s)

Peptide standard

Description

Format

Details

Author(s)

See Also

Examples

Method for Function plot in Package specL

Description

Value

Methods

BiblioSpec Reader

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Methods for Function show in Package specL ~~

Description

Methods

Class "specL"

Description

Objects from the Class

Slots

Methods

Note

Author(s)

See Also

Examples

Class "specLSet"

Description

Objects from the Class

Slots

Methods

Note

Author(s)

See Also

Examples

Method for Function `plot` in Package specL

Methods for Function `show` in Package specL ~~

Class `"specL"`

Class `"specLSet"`

Methods for Function `write.spectronaut` in Package specL