peaks: Access the raw data from an 'mzR' object.
In mzR: parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Description
Usage
Arguments
Details
Note
Author(s)
See Also
Examples
Description
Access the MS raw data. The peaks, spectra (can be used
interchangeably) and peaksCount functions return the (m/z,
intensity) pairs and the number peaks in the
spectrum/spectra. peaks and spectra return a single
matrix if scans is a numeric of length 1 and a list of
matrices if several scans are asked for or no scans argument is
provided (i.e all spectra in the oject are retured). peaksCount
will return a numeric of length n.
The header function returns a list containing
seqNum, acquisitionNum, msLevel,
peaksCount, totIonCurrent, retentionTime (in
seconds), basePeakMZ, basePeakIntensity,
collisionEnergy, ionisationEnergy, lowM,
highMZ, precursorScanNum, precursorMZ,
precursorCharge, precursorIntensity,
mergedScan, mergedResultScanNum,
mergedResultStartScanNum, mergedResultEndScanNum,
filterString, spectrumId, centroided
(logical whether the data of the spectrum is in centroid mode
or profile mode; only for pwiz backend), injectionTime (ion
injection time, in milliseconds), ionMobilityDriftTime (in
milliseconds), isolationWindowTargetMZ,
isolationWindowLowerOffset,
isolationWindowUpperOffset, scanWindowLowerLimit and
scanWindowUpperLimit. If multiple scans are queried, a
data.frame is returned with the scans reported along the
rows. For missing or not defined spectrum variables NA is reported.
The get3Dmap function performs a simple resampling between
lowMz and highMz with reMz resolution. A matrix
of dimensions length(scans) times
seq(lowMz,highMz,resMz) is returned.
The chromatogram (chromatograms) accessors return
chromatograms for the MS file handle. If a single index is provided,
as data.frame containing the retention time (1st columns) and
intensities (2nd column) is returned. The name of the former is always
time, while the latter will depend on the run parameters.
If more than 1 or no chromatogram indices are provided, then a list of
chromatograms is returned; either those passed as argument or all of
them. By default, the first (and possibly only) chromatogram is the
total ion count, which can also be accessed with the tic
method.
The nChrom function returns the number of chromatograms,
including the total ion chromatogram.
The chromatogramHeader returns (similar to the header
function for spectra) a data.frame with metadata information
for the individual chromatograms. The data.frame has the
columns: "chromatogramId" (the ID of the chromatogram as
specified in the file), "chromatogramIndex" (the index of the
chromatogram within the file), "polarity" (the polarity for the
chromatogram, 0 for negative, +1 for positive and -1 for not set),
"precursorIsolationWindowTargetMZ" (the isolation window m/z of
the precursor), "precursorIsolationWindowLowerOffset",
"precursorIsolationWindowUpperOffset" (lower and upper offset
for the isolation window m/z), "precursorCollisionEnergy"
(collision energy),
"productIsolationWindowTargetMZ",
"productIsolationWindowLowerOffset" and
"productIsolationWindowUpperOffset" (definition of the m/z
isolation window for the product).
Note that access to chromatograms is only supported in the pwiz
backend.
Usage
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header(object, scans, ...)
peaksCount(object, scans, ...)
## S4 method for signature 'mzRpwiz'
peaks(object, scans)
## S4 method for signature 'mzRramp'
peaks(object, scans)
## S4 method for signature 'mzRnetCDF'
peaks(object, scans)
## S4 method for signature 'mzRpwiz'
spectra(object, scans) ## same as peaks
## S4 method for signature 'mzRramp'
spectra(object, scans)
## S4 method for signature 'mzRnetCDF'
spectra(object, scans)
get3Dmap(object, scans, lowMz, highMz, resMz, ...)
## S4 method for signature 'mzRpwiz'
chromatogram(object, chrom)
## S4 method for signature 'mzRpwiz'
chromatograms(object, chrom) ## same as chromatogram
## S4 method for signature 'mzRpwiz'
chromatogramHeader(object, chrom)
tic(object, ...)
nChrom(object)
Arguments
object
An instantiated mzR object.
scans
A numeric specifying which scans to
return. Optional for the header, peaks, spectra
and peaksCount methods. If ommited, the requested data for
all peaks is returned.
lowMz, highMz
Numerics defining the m/z range to be
returned.
resMz
a numeric defining the m/z resolution.
chrom
For chromatogram, chromatograms and
chromatogramHeader: numeric specifying the index
of the chromatograms to be extracted from the file. If omitted, data
for all chromatograms is returned.
...
Other arguments. A scan parameter can be passed to
peaks.
Details
The column acquisitionNum in the data.frame returned by
the header method contains the index during the scan in which
the signal from the spectrum was measured. The pwiz backend
extracts this number from the spectrum's ID provided in the mzML
file. In contrast, column seqNum contains the index of each
spectrum within the file and is thus consecutively numbered. Spectra
from files with multiple MS levels are linked to each other via
their acquisitionNum: column precursorScanNum of an e.g. MS
level 2 spectrum contains the acquisitionNum of the related MS
level 1 spectrum.
Note
Spectrum identifiers are only specified in mzML files, thus,
for all other file types the column "spectrumId" of the result
data.frame returned by header contains "scan="
followed by the acquisition number of the spectrum. Also, only the
pwiz backend supports extraction of the spectras' IDs from
mzML files. Thus, only mzML files read with
backend = "pwiz" provide the spectrum IDs defined in the file.
The content of the spectrum identifier depends on the vendor and the
instrument acquisition settings and is reported here as a character,
in its raw form, without further parsing.
Author(s)
Steffen Neumann and Laurent Gatto
See Also
instrumentInfo for metadata access and the
"mzR" class.
writeMSData and copyWriteMSData for
functions to write MS data in mzML or mzXML format.
Examples
1
2
3
4
5
6
7
8
9
10
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13
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34
library(msdata)
filepath <- system.file("microtofq", package = "msdata")
file <- list.files(filepath, pattern="MM14.mzML",
full.names=TRUE, recursive = TRUE)
mz <- openMSfile(file)
runInfo(mz)
colnames(header(mz))
close(mz)
## A shotgun LCMSMS experiment
f <- proteomics(full.names = TRUE,
pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
x <- openMSfile(f, backend = "pwiz")
x
nChrom(x)
head(tic(x))
head(chromatogram(x, 1L)) ## same as tic(x)
str(chromatogram(x)) ## as a list
p <- peaks(x) ## extract all peak information
head(peaks(x, scan=4)) ## extract just peaks from the 4th scan
## An MRM experiment
f <- proteomics(full.names = TRUE, pattern = "MRM")
x <- openMSfile(f, backend = "pwiz")
x
nChrom(x)
head(tic(x))
head(chromatogram(x, 1L)) ## same as tic(x)
str(chromatogram(x, 10:12))
## get the header information for the chromatograms
ch <- chromatogramHeader(x)
head(ch)
Example output
Loading required package: Rcpp
$scanCount
[1] 112
$lowMz
[1] 0
$highMz
[1] 0
$dStartTime
[1] 270.334
$dEndTime
[1] 307.678
$msLevels
[1] 1
$startTimeStamp
[1] NA
[1] "seqNum" "acquisitionNum"
[3] "msLevel" "polarity"
[5] "peaksCount" "totIonCurrent"
[7] "retentionTime" "basePeakMZ"
[9] "basePeakIntensity" "collisionEnergy"
[11] "ionisationEnergy" "lowMZ"
[13] "highMZ" "precursorScanNum"
[15] "precursorMZ" "precursorCharge"
[17] "precursorIntensity" "mergedScan"
[19] "mergedResultScanNum" "mergedResultStartScanNum"
[21] "mergedResultEndScanNum" "injectionTime"
[23] "filterString" "spectrumId"
[25] "centroided" "ionMobilityDriftTime"
[27] "isolationWindowTargetMZ" "isolationWindowLowerOffset"
[29] "isolationWindowUpperOffset" "scanWindowLowerLimit"
[31] "scanWindowUpperLimit"
Mass Spectrometry file handle.
Filename: TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
Number of scans: 509
[1] 1
time TIC
1 0.00764000 9187505
2 0.01620833 9118685
3 0.03087333 9247653
4 0.04570667 9195261
5 0.06020667 9202081
6 0.07487500 9451720
time TIC
1 0.00764000 9187505
2 0.01620833 9118685
3 0.03087333 9247653
4 0.04570667 9195261
5 0.06020667 9202081
6 0.07487500 9451720
List of 1
$ :'data.frame': 7534 obs. of 2 variables:
..$ time: num [1:7534] 0.00764 0.01621 0.03087 0.04571 0.06021 ...
..$ TIC : num [1:7534] 9187505 9118685 9247653 9195261 9202081 ...
[,1] [,2]
[1,] 100.0999 467.1394
[2,] 100.5178 446.3754
[3,] 104.5826 406.7346
[4,] 110.0711 1762.0354
[5,] 111.9731 555.5806
[6,] 111.9800 385.0784
Mass Spectrometry file handle.
Filename: MRM-standmix-5.mzML.gz
Number of scans: 0
[1] 138
time TIC
1 1.666667e-05 45.37833
2 4.233333e-03 44.39301
3 8.450000e-03 45.33704
4 1.266667e-02 44.30909
5 1.686667e-02 45.40231
6 2.108333e-02 44.29813
time TIC
1 1.666667e-05 45.37833
2 4.233333e-03 44.39301
3 8.450000e-03 45.33704
4 1.266667e-02 44.30909
5 1.686667e-02 45.40231
6 2.108333e-02 44.29813
List of 3
$ :'data.frame': 1073 obs. of 2 variables:
..$ time : num [1:1073] 0.00423 0.01267 0.02108 0.02952 0.03795 ...
..$ X..SRM.SIC.Q1.134.Q3.91.996.start.0.004233333333.end.9.77305: num [1:1073] 44.4 44.3 44.3 44.1 44.1 ...
$ :'data.frame': 1073 obs. of 2 variables:
..$ time : num [1:1073] 1.67e-05 8.45e-03 1.69e-02 2.53e-02 3.37e-02 ...
..$ X..SRM.SIC.Q1.134.Q3.106.996.start.1.666666667e.005.end.9.772783333: num [1:1073] 45.4 45.3 45.4 45.6 45.6 ...
$ :'data.frame': 640 obs. of 2 variables:
..$ time : num [1:640] 3.46 3.47 3.48 3.49 3.5 ...
..$ X..SRM.SIC.Q1.135.Q3.64.996.start.3.461933333.end.9.467483333: num [1:640] 129 137 141 147 156 ...
chromatogramId
1 TIC
2 - SRM SIC Q1=89 Q3=40.996 start=5.21145 end=15.20321667
3 - SRM SIC Q1=89 Q3=42.996 start=5.211116667 end=15.20308333
4 - SRM SIC Q1=115 Q3=26.996 start=10.14841667 end=16.16721667
5 - SRM SIC Q1=115 Q3=70.996 start=10.14816667 end=16.16706667
6 - SRM SIC Q1=117 Q3=72.996 start=10.14793333 end=16.1428
chromatogramIndex polarity precursorIsolationWindowTargetMZ
1 1 -1 NA
2 2 0 89
3 3 0 89
4 4 0 115
5 5 0 115
6 6 0 117
precursorIsolationWindowLowerOffset precursorIsolationWindowUpperOffset
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
precursorCollisionEnergy productIsolationWindowTargetMZ
1 NA NA
2 20 40.996
3 10 42.996
4 10 26.996
5 2 70.996
6 10 72.996
productIsolationWindowLowerOffset productIsolationWindowUpperOffset
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
mzR documentation built on Nov. 20, 2020, 2 a.m.
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Description Usage Arguments Details Note Author(s) See Also Examples
Description
Access the MS raw data. The peaks, spectra (can be used
interchangeably) and peaksCount functions return the (m/z,
intensity) pairs and the number peaks in the
spectrum/spectra. peaks and spectra return a single
matrix if scans is a numeric of length 1 and a list of
matrices if several scans are asked for or no scans argument is
provided (i.e all spectra in the oject are retured). peaksCount
will return a numeric of length n.
The header function returns a list containing
seqNum, acquisitionNum, msLevel,
peaksCount, totIonCurrent, retentionTime (in
seconds), basePeakMZ, basePeakIntensity,
collisionEnergy, ionisationEnergy, lowM,
highMZ, precursorScanNum, precursorMZ,
precursorCharge, precursorIntensity,
mergedScan, mergedResultScanNum,
mergedResultStartScanNum, mergedResultEndScanNum,
filterString, spectrumId, centroided
(logical whether the data of the spectrum is in centroid mode
or profile mode; only for pwiz backend), injectionTime (ion
injection time, in milliseconds), ionMobilityDriftTime (in
milliseconds), isolationWindowTargetMZ,
isolationWindowLowerOffset,
isolationWindowUpperOffset, scanWindowLowerLimit and
scanWindowUpperLimit. If multiple scans are queried, a
data.frame is returned with the scans reported along the
rows. For missing or not defined spectrum variables NA is reported.
The get3Dmap function performs a simple resampling between
lowMz and highMz with reMz resolution. A matrix
of dimensions length(scans) times
seq(lowMz,highMz,resMz) is returned.
The chromatogram (chromatograms) accessors return
chromatograms for the MS file handle. If a single index is provided,
as data.frame containing the retention time (1st columns) and
intensities (2nd column) is returned. The name of the former is always
time, while the latter will depend on the run parameters.
If more than 1 or no chromatogram indices are provided, then a list of
chromatograms is returned; either those passed as argument or all of
them. By default, the first (and possibly only) chromatogram is the
total ion count, which can also be accessed with the tic
method.
The nChrom function returns the number of chromatograms,
including the total ion chromatogram.
The chromatogramHeader returns (similar to the header
function for spectra) a data.frame with metadata information
for the individual chromatograms. The data.frame has the
columns: "chromatogramId" (the ID of the chromatogram as
specified in the file), "chromatogramIndex" (the index of the
chromatogram within the file), "polarity" (the polarity for the
chromatogram, 0 for negative, +1 for positive and -1 for not set),
"precursorIsolationWindowTargetMZ" (the isolation window m/z of
the precursor), "precursorIsolationWindowLowerOffset",
"precursorIsolationWindowUpperOffset" (lower and upper offset
for the isolation window m/z), "precursorCollisionEnergy"
(collision energy),
"productIsolationWindowTargetMZ",
"productIsolationWindowLowerOffset" and
"productIsolationWindowUpperOffset" (definition of the m/z
isolation window for the product).
Note that access to chromatograms is only supported in the pwiz
backend.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | header(object, scans, ...)
peaksCount(object, scans, ...)
## S4 method for signature 'mzRpwiz'
peaks(object, scans)
## S4 method for signature 'mzRramp'
peaks(object, scans)
## S4 method for signature 'mzRnetCDF'
peaks(object, scans)
## S4 method for signature 'mzRpwiz'
spectra(object, scans) ## same as peaks
## S4 method for signature 'mzRramp'
spectra(object, scans)
## S4 method for signature 'mzRnetCDF'
spectra(object, scans)
get3Dmap(object, scans, lowMz, highMz, resMz, ...)
## S4 method for signature 'mzRpwiz'
chromatogram(object, chrom)
## S4 method for signature 'mzRpwiz'
chromatograms(object, chrom) ## same as chromatogram
## S4 method for signature 'mzRpwiz'
chromatogramHeader(object, chrom)
tic(object, ...)
nChrom(object)
|
Arguments
object |
An instantiated |
scans |
A |
lowMz, highMz |
|
resMz |
a |
chrom |
For |
... |
Other arguments. A |
Details
The column acquisitionNum in the data.frame returned by
the header method contains the index during the scan in which
the signal from the spectrum was measured. The pwiz backend
extracts this number from the spectrum's ID provided in the mzML
file. In contrast, column seqNum contains the index of each
spectrum within the file and is thus consecutively numbered. Spectra
from files with multiple MS levels are linked to each other via
their acquisitionNum: column precursorScanNum of an e.g. MS
level 2 spectrum contains the acquisitionNum of the related MS
level 1 spectrum.
Note
Spectrum identifiers are only specified in mzML files, thus,
for all other file types the column "spectrumId" of the result
data.frame returned by header contains "scan="
followed by the acquisition number of the spectrum. Also, only the
pwiz backend supports extraction of the spectras' IDs from
mzML files. Thus, only mzML files read with
backend = "pwiz" provide the spectrum IDs defined in the file.
The content of the spectrum identifier depends on the vendor and the
instrument acquisition settings and is reported here as a character,
in its raw form, without further parsing.
Author(s)
Steffen Neumann and Laurent Gatto
See Also
instrumentInfo for metadata access and the
"mzR" class.
writeMSData and copyWriteMSData for
functions to write MS data in mzML or mzXML format.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | library(msdata)
filepath <- system.file("microtofq", package = "msdata")
file <- list.files(filepath, pattern="MM14.mzML",
full.names=TRUE, recursive = TRUE)
mz <- openMSfile(file)
runInfo(mz)
colnames(header(mz))
close(mz)
## A shotgun LCMSMS experiment
f <- proteomics(full.names = TRUE,
pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
x <- openMSfile(f, backend = "pwiz")
x
nChrom(x)
head(tic(x))
head(chromatogram(x, 1L)) ## same as tic(x)
str(chromatogram(x)) ## as a list
p <- peaks(x) ## extract all peak information
head(peaks(x, scan=4)) ## extract just peaks from the 4th scan
## An MRM experiment
f <- proteomics(full.names = TRUE, pattern = "MRM")
x <- openMSfile(f, backend = "pwiz")
x
nChrom(x)
head(tic(x))
head(chromatogram(x, 1L)) ## same as tic(x)
str(chromatogram(x, 10:12))
## get the header information for the chromatograms
ch <- chromatogramHeader(x)
head(ch)
|
Example output
Loading required package: Rcpp
$scanCount
[1] 112
$lowMz
[1] 0
$highMz
[1] 0
$dStartTime
[1] 270.334
$dEndTime
[1] 307.678
$msLevels
[1] 1
$startTimeStamp
[1] NA
[1] "seqNum" "acquisitionNum"
[3] "msLevel" "polarity"
[5] "peaksCount" "totIonCurrent"
[7] "retentionTime" "basePeakMZ"
[9] "basePeakIntensity" "collisionEnergy"
[11] "ionisationEnergy" "lowMZ"
[13] "highMZ" "precursorScanNum"
[15] "precursorMZ" "precursorCharge"
[17] "precursorIntensity" "mergedScan"
[19] "mergedResultScanNum" "mergedResultStartScanNum"
[21] "mergedResultEndScanNum" "injectionTime"
[23] "filterString" "spectrumId"
[25] "centroided" "ionMobilityDriftTime"
[27] "isolationWindowTargetMZ" "isolationWindowLowerOffset"
[29] "isolationWindowUpperOffset" "scanWindowLowerLimit"
[31] "scanWindowUpperLimit"
Mass Spectrometry file handle.
Filename: TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
Number of scans: 509
[1] 1
time TIC
1 0.00764000 9187505
2 0.01620833 9118685
3 0.03087333 9247653
4 0.04570667 9195261
5 0.06020667 9202081
6 0.07487500 9451720
time TIC
1 0.00764000 9187505
2 0.01620833 9118685
3 0.03087333 9247653
4 0.04570667 9195261
5 0.06020667 9202081
6 0.07487500 9451720
List of 1
$ :'data.frame': 7534 obs. of 2 variables:
..$ time: num [1:7534] 0.00764 0.01621 0.03087 0.04571 0.06021 ...
..$ TIC : num [1:7534] 9187505 9118685 9247653 9195261 9202081 ...
[,1] [,2]
[1,] 100.0999 467.1394
[2,] 100.5178 446.3754
[3,] 104.5826 406.7346
[4,] 110.0711 1762.0354
[5,] 111.9731 555.5806
[6,] 111.9800 385.0784
Mass Spectrometry file handle.
Filename: MRM-standmix-5.mzML.gz
Number of scans: 0
[1] 138
time TIC
1 1.666667e-05 45.37833
2 4.233333e-03 44.39301
3 8.450000e-03 45.33704
4 1.266667e-02 44.30909
5 1.686667e-02 45.40231
6 2.108333e-02 44.29813
time TIC
1 1.666667e-05 45.37833
2 4.233333e-03 44.39301
3 8.450000e-03 45.33704
4 1.266667e-02 44.30909
5 1.686667e-02 45.40231
6 2.108333e-02 44.29813
List of 3
$ :'data.frame': 1073 obs. of 2 variables:
..$ time : num [1:1073] 0.00423 0.01267 0.02108 0.02952 0.03795 ...
..$ X..SRM.SIC.Q1.134.Q3.91.996.start.0.004233333333.end.9.77305: num [1:1073] 44.4 44.3 44.3 44.1 44.1 ...
$ :'data.frame': 1073 obs. of 2 variables:
..$ time : num [1:1073] 1.67e-05 8.45e-03 1.69e-02 2.53e-02 3.37e-02 ...
..$ X..SRM.SIC.Q1.134.Q3.106.996.start.1.666666667e.005.end.9.772783333: num [1:1073] 45.4 45.3 45.4 45.6 45.6 ...
$ :'data.frame': 640 obs. of 2 variables:
..$ time : num [1:640] 3.46 3.47 3.48 3.49 3.5 ...
..$ X..SRM.SIC.Q1.135.Q3.64.996.start.3.461933333.end.9.467483333: num [1:640] 129 137 141 147 156 ...
chromatogramId
1 TIC
2 - SRM SIC Q1=89 Q3=40.996 start=5.21145 end=15.20321667
3 - SRM SIC Q1=89 Q3=42.996 start=5.211116667 end=15.20308333
4 - SRM SIC Q1=115 Q3=26.996 start=10.14841667 end=16.16721667
5 - SRM SIC Q1=115 Q3=70.996 start=10.14816667 end=16.16706667
6 - SRM SIC Q1=117 Q3=72.996 start=10.14793333 end=16.1428
chromatogramIndex polarity precursorIsolationWindowTargetMZ
1 1 -1 NA
2 2 0 89
3 3 0 89
4 4 0 115
5 5 0 115
6 6 0 117
precursorIsolationWindowLowerOffset precursorIsolationWindowUpperOffset
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
precursorCollisionEnergy productIsolationWindowTargetMZ
1 NA NA
2 20 40.996
3 10 42.996
4 10 26.996
5 2 70.996
6 10 72.996
productIsolationWindowLowerOffset productIsolationWindowUpperOffset
1 NA NA
2 NA NA
3 NA NA
4 NA NA
5 NA NA
6 NA NA
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