Package 'rawrr' reference manual

Title:	Direct Access to Orbitrap Data and Beyond
Description:	This package wraps the functionality of the RawFileReader .NET assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.
Authors:	Christian Panse [aut, cre] , Tobias Kockmann [aut]
Maintainer:	Christian Panse <[email protected]>
License:	GPL-3
Version:	1.13.1
Built:	2024-09-20 11:37:48 UTC
Source:	https://github.com/bioc/rawrr

Check if a file is contained in the environment variable `MONO_PATH`.

Description

Check if a file is contained in the environment variable MONO_PATH.

Usage

.checkDllInMonoPath(dll = "ThermoFisher.CommonCore.Data.dll")
.checkDllInMonoPath(dll = "ThermoFisher.CommonCore.Data.dll")

Arguments

dll

a file name.

Value

a boolean

URL for Thermo Fisher .NET assemblies

Description

URL for Thermo Fisher .NET assemblies

Usage

.thermofisherlsmsUrl()
.thermofisherlsmsUrl()

Value

an URL

deriving area under the curve (AUC)

Description

deriving area under the curve (AUC)

Usage

auc.rawrrChromatogram(x)
auc.rawrrChromatogram(x)

Arguments

`x`	an rawrrChromatogram object contains `x$times` and `x$intensities`. `x$times` is assumed to be in minutes.

Value

A numeric value.

Base peak of a spectrum

Description

Base peak of a spectrum

Usage

basePeak(x)
basePeak(x)

Arguments

`x`	A rawrrSpectrum object

Value

A double vector of length two. The first component is the base peak position (m/z). The second component is the base peak intensity.

Examples

S <- readSpectrum(rawfile = sampleFilePath(), 1)
basePeak(S[[1]])
S <- readSpectrum(rawfile = sampleFilePath(), 1)
basePeak(S[[1]])

Build `rawrr.exe` console application.

Description

builds rawrr.exe file from C# source code requiring xbuild or msbuild tools. The console application rawrr.exe is used by the package's reader functions through a system2 call.

Usage

buildRawrrExe()
buildRawrrExe()

Details

The rawrr package implementation consists of two language layers, the top R layer and the hidden C# layer. Specifically, R functions requesting access to data stored in binary raw files invoke compiled C# wrapper methods using a system2 call. Calling a wrapper method typically results in the execution of methods defined in the RawFileReader dynamic link library provided by Thermo Fisher Scientific. Our precompiled wrapper methods are bundled in the rawrr.exe executable file (.NET assembly) and shipped with the released R package. Running rawrr.exe requires the https://www.mono-project.com/ environment on non-Microsoft operating systems. Mono is a cross platform, open source .NET framework. On Microsoft Windows the Microsoft .NET framework is typically already installed and sufficient. Our package also contains the C# source code rawrr.cs. In order to return extracted data back to the R layer we use file I/O. More specifically, the extracted information is written to a temporary location on the harddrive, read back into memory and parsed into R objects.

Value

the return value of the system2 command.

Author(s)

Tobias Kockmann, Christian Panse <[email protected]>, 2021

References

Retrieve dependent scan(s) of a scan listed in scan index

Description

Retrieve dependent scan(s) of a scan listed in scan index

Usage

dependentScan(x, scanNumber)
dependentScan(x, scanNumber)

Arguments

`x`	A scan index returned by `readIndex`.
`scanNumber`	The scan number that should be inspected for dependent scans.

Value

The scan number of the dependent scan(s).

Examples

Idx <- readIndex(rawfile = sampleFilePath())
dependentScan(Idx, scanNumber = 1)
Idx <- readIndex(rawfile = sampleFilePath())
dependentScan(Idx, scanNumber = 1)

Is FAIMS Voltage on?

Description

Is FAIMS Voltage on?

Usage

faimsVoltageOn(x)
faimsVoltageOn(x)

Arguments

`x`	A rawrrSpectrum object

Value

A boolean

Examples

S <- readSpectrum(rawfile = sampleFilePath(), 1:10)
try(faimsVoltageOn(S[[1]]))
S <- readSpectrum(rawfile = sampleFilePath(), 1:10)
try(faimsVoltageOn(S[[1]]))

determine scan numbers which match a specified filter

Description

determine scan numbers which match a specified filter

Usage

filter(rawfile, filter = "ms", precision = 10, tmpdir = tempdir())
filter(rawfile, filter = "ms", precision = 10, tmpdir = tempdir())

Arguments

`rawfile`	the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
`filter`	scan filter string, e.g., `ms` or `ms2`
`precision`	mass precision, default is 10.
`tmpdir`	defines the directory used to store temporary data generated by the .NET assembly `rawrr.exe`. The default uses the output of `tempdir()`.

Value

a vecntor of integer values.

Download and install the New RawFileReader from Thermo Fisher Scientific .Net assemblies i

Description

Download and install the New RawFileReader from Thermo Fisher Scientific .Net assemblies in the directory provided by rawrrAssemblyPath().

Usage

installRawFileReaderDLLs(sourceUrl = .thermofisherlsmsUrl(), ...)
installRawFileReaderDLLs(sourceUrl = .thermofisherlsmsUrl(), ...)

Arguments

`sourceUrl`	url of New RawFileReader from Thermo Fisher Scientific assemblies.
`...`	other parameter for `download.file`

Details

The console application assembly rawrr.exe requires three assemplies:

ThermoFisher.CommonCore.Data.dll,
ThermoFisher.CommonCore.MassPrecisionEstimator.dll, and
ThermoFisher.CommonCore.RawFileReader.dll

The rawrr.exe assembly can be built from C# source code by using the msbuild tool shipped by the https://www.mono-project.com or by Microsoft's .NET SDK https://dotnet.microsoft.com on Linux, Microsoft, and macOS.

If no build tool and C# compiler (csc or msc) are available or the build process fails, you can download rawrr.exe assembly from the authors' site.

Value

An (invisible) vector of integer code, 0 for success and non-zero for failure. For the "wget" and "curl" methods this is the status code returned by the external program.

Author(s)

Christian Panse <[email protected]>, 2021

References

Examples

# to install all assemblies

rawrr::installRawFileReaderDLLs() 
rawrr::buildRawrrExe() || rawrr::installRawrrExe()

# to install all assemblies

rawrr::installRawFileReaderDLLs() 
rawrr::buildRawrrExe() || rawrr::installRawrrExe()

Download and install the `rawrr.exe` console application

Description

downloads and installs the rawrr.exe .Net assembly in the directory provided by rawrrAssemblyPath().

Usage

installRawrrExe(
  sourceUrl = "https://github.com/fgcz/rawrr/releases/download/1.9.2/rawrr.1.9.2.exe",
  ...
)
installRawrrExe(
  sourceUrl = "https://github.com/fgcz/rawrr/releases/download/1.9.2/rawrr.1.9.2.exe",
  ...
)

Arguments

`sourceUrl`	url of `rawrr.exe` assembly.
`...`	other parameter for `download.file`.

Details

The console application rawrr.exe is used by the package's reader functions through a system2 call.

Value

An integer code, 0 for success and non-zero for failure. For the "wget" and "curl" methods this is the status code returned by the external program.

References

doi:10.1021/acs.jproteome.0c00866

Function to check if an object is an instance of class `rawrrChromatogram`

Description

Function to check if an object is an instance of class rawrrChromatogram

Usage

is.rawrrChromatogram(x)
is.rawrrChromatogram(x)

Arguments

`x`	x any R object to be tested.

Value

TRUE or FALSE

Author(s)

Tobias Kockmann, 2020.

Examples

rawfile <- sampleFilePath()
C <- readChromatogram(rawfile, mass = 445.1181, tol = 10)
is.rawrrChromatogram(C[[1]])
rawfile <- sampleFilePath()
C <- readChromatogram(rawfile, mass = 445.1181, tol = 10)
is.rawrrChromatogram(C[[1]])

Function to check if an object is an instance of class `rawrrSpectrum`

Description

Function to check if an object is an instance of class rawrrSpectrum

Usage

is.rawrrSpectrum(x)
is.rawrrSpectrum(x)

Arguments

`x`	any R object to be tested.

Value

TRUE or FALSE

Examples

S <- rawrr::sampleFilePath() |> rawrr::readSpectrum(scan = 1:10)
rawrr::is.rawrrSpectrum(S[[1]])
S <- rawrr::sampleFilePath() |> rawrr::readSpectrum(scan = 1:10)
rawrr::is.rawrrSpectrum(S[[1]])

Function to check if an object is an instance of class `rawrrSpectrumSet`

Description

Function to check if an object is an instance of class rawrrSpectrumSet

Usage

is.rawrrSpectrumSet(x)
is.rawrrSpectrumSet(x)

Arguments

`x`	any R object to be tested.

Value

TRUE or FALSE

Examples

rawrr::sampleFilePath() |>
  rawrr::readSpectrum(scan = 1:10) |>
  rawrr::is.rawrrSpectrumSet()
rawrr::sampleFilePath() |>
  rawrr::readSpectrum(scan = 1:10) |>
  rawrr::is.rawrrSpectrumSet()

Make accessor function for key value pair returned by RawFileReader

Description

Make accessor function for key value pair returned by RawFileReader

Usage

makeAccessor(key, returnType = "integer")
makeAccessor(key, returnType = "integer")

Arguments

`key`	An object name found in instance of class `rawrrSpectrum`
`returnType`	The type used for casting of values

Details

This function factory creates accessor functions for class rawrrSpectrum.

Value

An accessor function

Author(s)

Tobias Kockmann, 2020

Examples

S <- readSpectrum(rawfile = sampleFilePath(), 1:10)
maxIonTime <- makeAccessor(key = "Max. Ion Time (ms):", returnType = "double")
maxIonTime(S[[1]])
S <- readSpectrum(rawfile = sampleFilePath(), 1:10)
maxIonTime <- makeAccessor(key = "Max. Ion Time (ms):", returnType = "double")
maxIonTime(S[[1]])

Acquisition/scan range of spectrum

Description

Acquisition/scan range of spectrum

Usage

massRange(x)
massRange(x)

Arguments

`x`	A rawrrSpectrum object

Value

A double vector of length two. The first component is the start m/z, the second is the stop m/z value used by the detector during data acquisition. Also referred to as scan range.

Examples

S <- readSpectrum(rawfile = sampleFilePath(), 1)
massRange(S[[1]])
S <- readSpectrum(rawfile = sampleFilePath(), 1)
massRange(S[[1]])

Retrieve master scan of scan listed in scan index

Description

Retrieve master scan of scan listed in scan index

Usage

masterScan(x, scanNumber)
masterScan(x, scanNumber)

Arguments

`x`	A scan index returned by `readIndex`.
`scanNumber`	The scan number that should be inspected for the presence of a master scan.

Value

Returns the scan number of the master scan or NA if no master scan exists.

Examples

rawrr::sampleFilePath() |>  rawrr::readIndex() |> rawrr::masterScan(scanNumber = 1)
rawrr::sampleFilePath() |>  rawrr::readIndex() |> rawrr::masterScan(scanNumber = 1)

Create instances of class `rawrrSpectrum`

Description

Developer function.

Usage

new_rawrrSpectrum(
  scan = numeric(),
  massRange = numeric(),
  scanType = character(),
  StartTime = numeric(),
  centroidStream = logical(),
  mZ = numeric(),
  intensity = numeric()
)
new_rawrrSpectrum(
  scan = numeric(),
  massRange = numeric(),
  scanType = character(),
  StartTime = numeric(),
  centroidStream = logical(),
  mZ = numeric(),
  intensity = numeric()
)

Arguments

`scan`	scan number
`massRange`	Mass range covered by spectrum
`scanType`	Character string describing the scan type.
`StartTime`	Retention time in minutes
`centroidStream`	Logical indicating if centroided data is available
`mZ`	m/z values
`intensity`	Intensity values

Value

Object of class rawrrSpectrum

Author(s)

Tobias Kockmann, 2020.

Plot `rawrrChromatogram` objects

Description

Plot rawrrChromatogram objects

Usage

## S3 method for class 'rawrrChromatogram'
plot(x, legend = TRUE, ...)
## S3 method for class 'rawrrChromatogram'
plot(x, legend = TRUE, ...)

Arguments

`x`	A `rawrrChromatogram` object to be plotted.
`legend`	Should legend be printed?
`...`	Passes additional arguments.

Value

This function creates a plot.

Author(s)

Tobias Kockmann, 2020.

Examples

rawfile <- sampleFilePath()
C <- readChromatogram(rawfile, mass = 445.1181, tol = 10)
plot(C[[1]])
rawfile <- sampleFilePath()
C <- readChromatogram(rawfile, mass = 445.1181, tol = 10)
plot(C[[1]])

Plot `rawrrChromatogramSet` objects

Description

Plot rawrrChromatogramSet objects

Usage

## S3 method for class 'rawrrChromatogramSet'
plot(x, diagnostic = FALSE, ...)
## S3 method for class 'rawrrChromatogramSet'
plot(x, diagnostic = FALSE, ...)

Arguments

`x`	A `rawrrChromatogramSet` object to be plotted.
`diagnostic`	Show diagnostic legend?
`...`	Passes additional arguments.

Value

This function creates a plot.

Author(s)

Tobias Kockmann, 2020.

Basic plotting function for instances of `rawrrSpectrum`

Description

Plot method for objects of class rawrrSpectrum.

Usage

## S3 method for class 'rawrrSpectrum'
plot(
  x,
  relative = TRUE,
  centroid = FALSE,
  SN = FALSE,
  legend = TRUE,
  diagnostic = FALSE,
  ...
)
## S3 method for class 'rawrrSpectrum'
plot(
  x,
  relative = TRUE,
  centroid = FALSE,
  SN = FALSE,
  legend = TRUE,
  diagnostic = FALSE,
  ...
)

Arguments

`x`	an object of class `rawrrSpectrum`.
`relative`	If set to `TRUE` enforces plotting of relative intensities rather than absolute.
`centroid`	Should centroided data be used for plotting?
`SN`	Should Signal/Noise be used for plotting?
`legend`	Should legend be printed?
`diagnostic`	Should this option be applied? The default is `FALSE`.
`...`	function passes arbitrary additional arguments.

Details

plot.rawrrSpectrum is a low level function that calls base::plot for plotting rawrrSpectrum objects. It passes all additional arguments to plot()

Is usually called by method dispatch.

Value

This function creates a plot.

Author(s)

Tobias Kockmann, 2020.

Print method imitate the look and feel of Thermo Fisher Scientific FreeStyle's output

Description

Print method imitate the look and feel of Thermo Fisher Scientific FreeStyle's output

Usage

## S3 method for class 'rawrrSpectrum'
print(x, ...)
## S3 method for class 'rawrrSpectrum'
print(x, ...)

Arguments

`x`	an `rawrrSpectrum` object.
`...`	Arguments to be passed to methods.

Value

This function creates a print message.

Author(s)

Christian Panse and Tobias Kockmann, 2020.

Derives the path where all .NET assemblies are stored.

Description

Derives the path where all .NET assemblies are stored.

Usage

rawrrAssemblyPath()
rawrrAssemblyPath()

Value

path

Examples

rawrrAssemblyPath()
rawrrAssemblyPath()

Create `rawrrSpectrum` objects

Description

High-level constructor for instances of class rawrrSpectrum, also named helper function. Currently, mainly to support testing and for demonstration.

Usage

rawrrSpectrum(sim = "TESTPEPTIDE")
rawrrSpectrum(sim = "TESTPEPTIDE")

Arguments

sim

Either example_1 or TESTPEPTIDE

Value

Function returns a validated rawrrSpectrum object

Author(s)

Tobias Kockmann, 2020.

Examples

plot(rawrrSpectrum(sim = "TESTPEPTIDE"))
rawrrSpectrum(sim = "example_1")

plot(rawrrSpectrum(sim = "TESTPEPTIDE"))
rawrrSpectrum(sim = "example_1")

Extracts chromatographic data from a raw file.

Description

Extracts chromatographic data from a raw file.

Usage

readChromatogram(
  rawfile,
  mass = NULL,
  tol = 10,
  filter = "ms",
  type = "xic",
  tmpdir = tempdir()
)
readChromatogram(
  rawfile,
  mass = NULL,
  tol = 10,
  filter = "ms",
  type = "xic",
  tmpdir = tempdir()
)

Arguments

`rawfile`	the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
`mass`	a vector of mass values iff `type = 'xic'`.
`tol`	mass tolerance in ppm iff `type = 'xic'`.
`filter`	defines the scan filter, default is `filter="ms"` if a wrong filter is set the function will return `NULL` and draws a warning.
`type`	`c(xic, bpc, tic)` for extracted ion , base peak or total ion chromatogram.
`tmpdir`	defines the directory used to store temporary data generated by the .NET assembly `rawrr.exe`. The default uses the output of `tempdir()`.

Details

Chromatograms come in different flavors but are always signal intensity values as a function of time. Signal intensities can be point estimates from scanning detectors or plain intensities from non-scanning detectors, e.g., UV trace. Scanning detector (mass analyzers) point estimates can be defined in different ways by, for instance, summing all signals of a given spectrum (total ion chromatogram or TIC), or by extracting signal around an expected value (extracted ion chromatogram = XIC), or by using the maximum signal contained in a spectrum (base peak chromatogram = BPC). On top, chromatograms can be computed from pre-filtered lists of scans. A total ion chromatogram (TIC), for instance, is typically generated by iterating over all MS1-level scans.

Value

chromatogram object(s) containing of a vector of times and a corresponding vector of intensities.

Author(s)

Christian Trachsel, Tobias Kockmann and Christian Panse <[email protected]> 2018, 2019, 2020.

References

Automated quality control sample 1 (autoQC01) analyzed across different Thermo Scientific mass spectrometers, MSV000086542.

Examples


# Example 1: not meaningful but proof-of-concept
(rawfile <- rawrr::sampleFilePath())

rawrr::readChromatogram(rawfile, mass=c(669.8381, 726.8357), tol=1000) |>
    plot()
rawrr::readChromatogram(rawfile, type='bpc') |> plot()
rawrr::readChromatogram(rawfile, type='tic') |> plot()

# Example 2: extract iRT peptides
 if (require(ExperimentHub) & require(protViz)){
iRTpeptide <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR",
  "GAGSSEPVTGLDAK", "TPVISGGPYEYR", "VEATFGVDESNAK",
  "TPVITGAPYEYR", "DGLDAASYYAPVR", "ADVTPADFSEWSK",
  "LFLQFGAQGSPFLK")


# fetch via ExperimentHub
library(ExperimentHub)
eh <- ExperimentHub::ExperimentHub()
EH4547 <- normalizePath(eh[["EH4547"]])

(rawfile <- paste0(EH4547, ".raw"))
if (!file.exists(rawfile)){
    file.link(EH4547, rawfile)
}
op <- par(mfrow=c(2,1))
readChromatogram(rawfile, type='bpc') |> plot()
readChromatogram(rawfile, type='tic') |> plot()
par(op)

# derive [2H+] ions
((protViz::parentIonMass(iRTpeptide) + 1.008) / 2) |>
   readChromatogram(rawfile=rawfile) |>
   plot()
}
# Example 1: not meaningful but proof-of-concept
(rawfile <- rawrr::sampleFilePath())

rawrr::readChromatogram(rawfile, mass=c(669.8381, 726.8357), tol=1000) |>
    plot()
rawrr::readChromatogram(rawfile, type='bpc') |> plot()
rawrr::readChromatogram(rawfile, type='tic') |> plot()

# Example 2: extract iRT peptides
 if (require(ExperimentHub) & require(protViz)){
iRTpeptide <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR",
  "GAGSSEPVTGLDAK", "TPVISGGPYEYR", "VEATFGVDESNAK",
  "TPVITGAPYEYR", "DGLDAASYYAPVR", "ADVTPADFSEWSK",
  "LFLQFGAQGSPFLK")


# fetch via ExperimentHub
library(ExperimentHub)
eh <- ExperimentHub::ExperimentHub()
EH4547 <- normalizePath(eh[["EH4547"]])

(rawfile <- paste0(EH4547, ".raw"))
if (!file.exists(rawfile)){
    file.link(EH4547, rawfile)
}
op <- par(mfrow=c(2,1))
readChromatogram(rawfile, type='bpc') |> plot()
readChromatogram(rawfile, type='tic') |> plot()
par(op)

# derive [2H+] ions
((protViz::parentIonMass(iRTpeptide) + 1.008) / 2) |>
   readChromatogram(rawfile=rawfile) |>
   plot()
}

read file header Information

Description

This function extracts the meta information from a given raw file.

Usage

readFileHeader(rawfile)
readFileHeader(rawfile)

Arguments

rawfile

the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.

Value

A list object containing the following entries: RAW file version, Creation date, Operator, Number of instruments, Description, Instrument model, Instrument name, Serial number, Software version, Firmware version, Units, Mass resolution, Number of scans, Number of ms2 scans, Scan range, Time range, Mass range, Scan filter (first scan), Scan filter (last scan), Total number of filters, Sample name, Sample id, Sample type, Sample comment, Sample vial, Sample volume, Sample injection volume, Sample row number, Sample dilution factor, or Sample barcode.

Author(s)

Tobias Kockmann and Christian Panse 2018, 2019, 2020.

References

Thermo Fisher Scientific's NewRawfileReader C# code snippets https://planetorbitrap.com/rawfilereader.

Examples

rawrr::sampleFilePath() |> readFileHeader()
rawrr::sampleFilePath() |> readFileHeader()

Read scan index

Description

Read scan index

Usage

readIndex(rawfile)
readIndex(rawfile)

Arguments

rawfile

the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.

Value

returns a data.frame with the column names scan, scanType, StartTime, precursorMass, MSOrder, charge, masterScan, and dependencyType of all spectra.

Author(s)

Tobias Kockmann and Christian Panse <[email protected]>, 2020, 2021

Examples

Idx <- rawrr::sampleFilePath() |> rawrr::readIndex()
table(Idx$scanType)
plot(Idx$StartTime, Idx$precursorMass, col=as.factor(Idx$charge), pch=16)

table(Idx$MSOrder)
Idx <- rawrr::sampleFilePath() |> rawrr::readIndex()
table(Idx$scanType)
plot(Idx$StartTime, Idx$precursorMass, col=as.factor(Idx$charge), pch=16)

table(Idx$MSOrder)

Reads spectral data from a raw file.

Description

The function derives spectra of a given raw file and a given vector of scan numbers.

Usage

readSpectrum(
  rawfile,
  scan = NULL,
  tmpdir = tempdir(),
  validate = FALSE,
  mode = ""
)
readSpectrum(
  rawfile,
  scan = NULL,
  tmpdir = tempdir(),
  validate = FALSE,
  mode = ""
)

Arguments

`rawfile`	the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
`scan`	a vector of requested scan numbers.
`tmpdir`	defines the directory used to store temporary data generated by the .NET assembly `rawrr.exe`. The default uses the output of `tempdir()`.
`validate`	boolean default is `FALSE`.
`mode`	if `mode = "barebone"` only mZ (centroidStream.Masses), intensity (centroidStream.Intensities), pepmass, StartTime and charge state is returned. As default mode is `""`.

Details

All mass spectra are recorded by scanning detectors (mass analyzers) that log signal intensities for ranges of mass to charge ratios (m/z), also referred to as position. These recordings can be of continuous nature, so-called profile data (p), or appear centroided (c) in case discrete information (tuples of position and intensity values) are sufficient. This heavily compacted data structure is often called a peak list. In addition to signal intensities, a peak list can also cover additional peak attributes like peak resolution (R), charge (z), or local noise estimates. In short, the additional attributes further described the nature of the original profile signal or help to group peak lists with respect to their molecular nature or processing history. A well-known example is the assignment of peaks to peak groups that constitute isotope patterns (M, M+1, M+2, ...). The names of objects encapsulated within rawrrSpectrum instances are keys returned by the Thermo Fisher Scientific New RawFileReader API and the corresponding values become data parts of the objects, typically vectors.

Value

a nested list of rawrrSpectrum objects containing more than 50 values of scan information, e.g., the charge state, two vectors containing the mZ and its corresponding intensity values or the AGC information, mass calibration, ion optics ...

Author(s)

Tobias Kockmann and Christian Panse <[email protected]> 2018, 2019, 2020, 2021

References

C# code snippets of the NewRawfileReader library https://planetorbitrap.com/rawfilereader.
rawrr: doi:10.1021/acs.jproteome.0c00866
Universal Spectrum Explorer: https://www.proteomicsdb.org/use/ doi:10.1021/acs.jproteome.1c00096

Examples


# Example 1
S <- rawrr::sampleFilePath() |> rawrr::readSpectrum(scan = 1:9)

S[[1]]

names(S[[1]])

plot(S[[1]])



# Example 2 - find best peptide spectrum match using the |> pipe operator
# fetch via ExperimentHub

if (require(ExperimentHub) & require(protViz)){
eh <- ExperimentHub::ExperimentHub()
EH4547 <- normalizePath(eh[["EH4547"]])

(rawfile <- paste0(EH4547, ".raw"))
if (!file.exists(rawfile)){
    file.link(EH4547, rawfile)
}

GAG <- "GAGSSEPVTGLDAK"

.bestPeptideSpectrumMatch <- function(rawfile,
    sequence="GAGSSEPVTGLDAK"){
    readIndex(rawfile) |>
        subset(abs((1.008 + (protViz::parentIonMass(sequence) - 1.008) / 2) -
            precursorMass) < 0.001, select = scan) |>
        unlist() |>
        readSpectrum(rawfile = rawfile) |>
        lapply(function(x) {
          y <- protViz::psm(sequence = GAG, spec=x, plot=FALSE);
          y$scan <- x$scan; y
        }) |>
        lapply(FUN= function(x){
          score <- sum(abs(x$mZ.Da.error) < 0.01);
          cbind(scan=x$scan, score=score)
        }) |>
        (function(x) as.data.frame(Reduce(rbind, x)))() |>
        subset(score > 0) |>
        (function(x) x[order(x$score, decreasing = TRUE),
            'scan'])() |>
        head(1)
}

start_time <- Sys.time()
bestMatch <- .bestPeptideSpectrumMatch(rawfile, GAG) |>
    rawrr::readSpectrum(rawfile=rawfile) |>
    lapply(function(x) protViz::peakplot(peptideSequence = GAG, x))

end_time <- Sys.time()
end_time - start_time

# Example 3
# using proteomicsdb \doi{10.1101/2020.09.08.287557}
# through https://www.proteomicsdb.org/use/

.UniversalSpectrumExplorer <- function(x, sequence){
    m <- protViz::psm( sequence, x)
    cat(paste(x$mZ[m$idx], "\t", x$intensity[m$idx]), sep = "\n")
}

rawrr::readSpectrum(rawfile=rawfile, 11091) |>
   lapply(function(x).UniversalSpectrumExplorer(x, sequence = GAG))
 }  
# Example 1
S <- rawrr::sampleFilePath() |> rawrr::readSpectrum(scan = 1:9)

S[[1]]

names(S[[1]])

plot(S[[1]])



# Example 2 - find best peptide spectrum match using the |> pipe operator
# fetch via ExperimentHub

if (require(ExperimentHub) & require(protViz)){
eh <- ExperimentHub::ExperimentHub()
EH4547 <- normalizePath(eh[["EH4547"]])

(rawfile <- paste0(EH4547, ".raw"))
if (!file.exists(rawfile)){
    file.link(EH4547, rawfile)
}

GAG <- "GAGSSEPVTGLDAK"

.bestPeptideSpectrumMatch <- function(rawfile,
    sequence="GAGSSEPVTGLDAK"){
    readIndex(rawfile) |>
        subset(abs((1.008 + (protViz::parentIonMass(sequence) - 1.008) / 2) -
            precursorMass) < 0.001, select = scan) |>
        unlist() |>
        readSpectrum(rawfile = rawfile) |>
        lapply(function(x) {
          y <- protViz::psm(sequence = GAG, spec=x, plot=FALSE);
          y$scan <- x$scan; y
        }) |>
        lapply(FUN= function(x){
          score <- sum(abs(x$mZ.Da.error) < 0.01);
          cbind(scan=x$scan, score=score)
        }) |>
        (function(x) as.data.frame(Reduce(rbind, x)))() |>
        subset(score > 0) |>
        (function(x) x[order(x$score, decreasing = TRUE),
            'scan'])() |>
        head(1)
}

start_time <- Sys.time()
bestMatch <- .bestPeptideSpectrumMatch(rawfile, GAG) |>
    rawrr::readSpectrum(rawfile=rawfile) |>
    lapply(function(x) protViz::peakplot(peptideSequence = GAG, x))

end_time <- Sys.time()
end_time - start_time

# Example 3
# using proteomicsdb \doi{10.1101/2020.09.08.287557}
# through https://www.proteomicsdb.org/use/

.UniversalSpectrumExplorer <- function(x, sequence){
    m <- protViz::psm( sequence, x)
    cat(paste(x$mZ[m$idx], "\t", x$intensity[m$idx]), sep = "\n")
}

rawrr::readSpectrum(rawfile=rawfile, 11091) |>
   lapply(function(x).UniversalSpectrumExplorer(x, sequence = GAG))
 }

Read and extract scan trailer from TFS raw files.

Description

Read and extract scan trailer from TFS raw files.

Usage

readTrailer(rawfile, label = NULL)
readTrailer(rawfile, label = NULL)

Arguments

`rawfile`	the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
`label`	if NULL; the function scans for all available labels.

Value

an vector of trailers or values of a given trailer. Of note, the values are usually returned as a character.

Examples

rawrr::sampleFilePath() |> rawrr:::readTrailer()
rawrr::sampleFilePath() |> rawrr:::readTrailer("AGC:") |> head()
rawrr::sampleFilePath() |> rawrr:::readTrailer()
rawrr::sampleFilePath() |> rawrr:::readTrailer("AGC:") |> head()

A small file size `sample.raw` BLOB

Description

The binary example file sample.raw, shipped with the package, contains 574 Fourier-transformed Orbitrap spectra (FTMS) recorded on a Thermo Fisher Scientific Q Exactive HF-X. The mass spectrometer was operated in line with a nano electrospray source (NSI) in positive mode (+). All spectra were written to disk after applying centroiding (c) and lock mass correction.

Usage

sampleFilePath()
sampleFilePath()

Details

Thermo Fisher Scientific Q Exactive HF-X raw file of size 1.5M bytes and checksum MD5 (sample.raw) = fe67058456c79af7442316c474d20e96. Additional raw data for demonstration and extended testing is available through MSV000086542 and the tartare package. Lions love raw meat!

Value

file path of the sample.raw location.

Author(s)

Tobias Kockmann, 2018, 2019.

References

Bioconductor tartare package.
Automated quality control sample 1 (autoQC01) analyzed across different Thermo Fisher Scientific mass spectrometers, MSV000086542.

Examples

sampleFilePath()
sampleFilePath()

Accessor function for scan number of `rawrrSpectrum` objects

Description

Accessor function for scan number of rawrrSpectrum objects

Usage

scanNumber(x)
scanNumber(x)

Arguments

`x`	A rawrrSpectrum object

Details

This accessor function returns the scan number of a mass spectrum stored as rawrrSpectrum object. Scan numbers are equal to the scan index $j$ running from 1 to $n$ with $n$ being the last scan of a raw file.

Value

The scan number of type integer

Examples

S <- readSpectrum(rawfile = sampleFilePath(), 1:10)
scanNumber(S[[1]])
S <- readSpectrum(rawfile = sampleFilePath(), 1:10)
scanNumber(S[[1]])

Text summary of chromatogram

Description

Text summary of chromatogram

Usage

## S3 method for class 'rawrrChromatogram'
summary(object, ...)
## S3 method for class 'rawrrChromatogram'
summary(object, ...)

Arguments

`object`	A `rawrrChromatogram` object
`...`	Function passes additional arguments.

Value

A rawrrChromatogram object

Examples

C <- readChromatogram(rawfile = sampleFilePath(),
mass = c(445.1181, 519.1367))
summary(C[[1]])
summary(C[[2]])
C <- readChromatogram(rawfile = sampleFilePath(),
mass = c(445.1181, 519.1367))
summary(C[[1]])
summary(C[[2]])

Basic summary function

Description

Basic summary function

Usage

## S3 method for class 'rawrrSpectrum'
summary(object, ...)
## S3 method for class 'rawrrSpectrum'
summary(object, ...)

Arguments

`object`	an `rawrrSpectrum` object.
`...`	Arguments to be passed to methods.

Value

This function creates a print message.

Author(s)

Christian Panse and Tobias Kockmann, 2020.

Total ion current of a spectrum

Description

Total ion current of a spectrum

Usage

tic(x)
tic(x)

Arguments

`x`	A rawrrSpectrum object

Value

A double vector of length one.

Examples

S <- readSpectrum(rawfile = sampleFilePath(), 1)
tic(S[[1]])
S <- readSpectrum(rawfile = sampleFilePath(), 1)
tic(S[[1]])

Validate output of the readIndex function

Description

Checks the validity of an readIndex returned object.

Usage

validate_rawrrIndex(x)
validate_rawrrIndex(x)

Arguments

`x`	object to be validated.

Value

Validated data.frame of readIndex object

Author(s)

Tobias Kockmann and Christian Panse, 2020-12-09.

Examples

rawrr::sampleFilePath() |> rawrr::readIndex() |> rawrr::validate_rawrrIndex() 
rawrr::sampleFilePath() |> rawrr::readIndex() |> rawrr::validate_rawrrIndex()

Validate instance of class rawrrSpectrum

Description

Checks the validity of rawrrSpectrum object attributes.

Usage

validate_rawrrSpectrum(x)
validate_rawrrSpectrum(x)

Arguments

`x`	object to be validated.

Value

Validated rawrrSpectrum object

Author(s)

Tobias Kockmann and Christian Panse, 2020.

Examples

S <- rawrr::sampleFilePath() |>
  rawrr::readSpectrum(scan = 1:9, validate=TRUE)
S <- rawrr::sampleFilePath() |>
  rawrr::readSpectrum(scan = 1:9, validate=TRUE)

Package 'rawrr'

Help Index

Check if a file is contained in the environment variable MONO_PATH.

Description

Usage

Arguments

Value

URL for Thermo Fisher .NET assemblies

Description

Usage

Value

deriving area under the curve (AUC)

Description

Usage

Arguments

Value

Base peak of a spectrum

Description

Usage

Arguments

Value

Examples

Build rawrr.exe console application.

Description

Usage

Details

Value

Author(s)

References

See Also

Retrieve dependent scan(s) of a scan listed in scan index

Description

Usage

Arguments

Value

Examples

Is FAIMS Voltage on?

Description

Usage

Arguments

Value

Examples

determine scan numbers which match a specified filter

Description

Usage

Arguments

Value

Download and install the New RawFileReader from Thermo Fisher Scientific .Net assemblies i

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Download and install the rawrr.exe console application

Description

Usage

Arguments

Details

Value

References

See Also

Function to check if an object is an instance of class rawrrChromatogram

Description

Usage

Arguments

Value

Author(s)

Examples

Function to check if an object is an instance of class rawrrSpectrum

Description

Usage

Arguments

Value

Examples

Function to check if an object is an instance of class rawrrSpectrumSet

Description

Check if a file is contained in the environment variable `MONO_PATH`.

Build `rawrr.exe` console application.

Download and install the `rawrr.exe` console application

Function to check if an object is an instance of class `rawrrChromatogram`

Function to check if an object is an instance of class `rawrrSpectrum`

Function to check if an object is an instance of class `rawrrSpectrumSet`

Create instances of class `rawrrSpectrum`

Plot `rawrrChromatogram` objects

Plot `rawrrChromatogramSet` objects

Basic plotting function for instances of `rawrrSpectrum`

Create `rawrrSpectrum` objects