The MsBackendMgf class supports import and export of MS/MS spectra data
from/to files in Mascot Generic Format
(mgf)
files. After initial import, the full MS data is kept in
memory. MsBackendMgf extends the Spectra::MsBackendDataFrame() backend
directly and supports thus the Spectra::applyProcessing() function to make
data manipulations persistent.
The MsBackendAnnotatedMgf class supports import of data from MGF files
that provide, in addition to the m/z and intensity values, also
additional annotations/metadata for each mass peak. For such MGF files it
is expected that each line contains information from a single mass peak,
separated by a white space (blank). The first two elements are expected to
be the peak's m/z and intensity values, while each additional element is
considered an annotation for this specific peak. See examples below for the
format of a supported MGF file. The backendInitialize() method of
MsBackendAnnotatedMgf does not support parameter nlines. Also, import
of data can be considerably slower compared to the standard MsBackendMgf
backend, because of the additionally required parsing of peak annotations.
Peaks information in MGF files are not named, thus, additional peaks
annotations are named using the standard naming convention for column named
of data frames: the first peaks annotation is called "V1", the second (if
available) "V2" and so on.
New objects are created with the MsBackendMgf() or
MsBackendAnnotatedMgf() function. The backendInitialize() method has to
be subsequently called to initialize the object and import the MS/MS data
from (one or more) MGF files.
The MsBackendMgf backend provides an export method that allows to export
the data from the Spectra object (parameter x) to a file in mgf format.
See the package vignette for details and examples.
Default mappings from fields in the MGF file to spectra variable names are
provided by the spectraVariableMapping() function. This function returns a
named character vector were names are the spectra variable names and the
values the respective field names in the MGF files. This named character
vector is submitted to the import and export function with parameter
mapping. It is also possible to pass own mappings (e.g. for special
MGF dialects) with the mapping parameter.
Usage
# S4 method for class 'MsBackendMgf'
backendInitialize(
object,
files,
mapping = spectraVariableMapping(object),
nlines = -1L,
...,
BPPARAM = SerialParam()
)
MsBackendMgf()
# S4 method for class 'MsBackendMgf'
spectraVariableMapping(object, format = c("mgf"))
# S4 method for class 'MsBackendMgf'
export(
object,
x,
file = tempfile(),
mapping = spectraVariableMapping(object),
exportTitle = TRUE,
...
)
# S4 method for class 'MsBackendAnnotatedMgf'
backendInitialize(
object,
files,
mapping = spectraVariableMapping(object),
...,
BPPARAM = SerialParam()
)
MsBackendAnnotatedMgf()Arguments
- object
Instance of
MsBackendMgfclass.- files
characterwith the (full) file name(s) of the mgf file(s) from which MS/MS data should be imported.- mapping
for
backendInitialize()andexport: namedcharactervector allowing to specify how fields from the MGF file should be renamed. Names are supposed to be the spectra variable name and values of the vector the field names in the MGF file. See output ofspectraVariableMapping()for the expected format and examples below or description above for details.- nlines
for
backendInitialize()ofMsBackendMgf:integer(1)defining the number of lines that should be imported and processed from the MGF file(s). By default (nlines = -1L) the full file is imported and processed at once. If set to a positive integer, the data is imported and processed chunk-wise usingreadMgfSplit().- ...
Currently ignored.
- BPPARAM
Parameter object defining the parallel processing setup. If parallel processing is enabled (with
BPPARAMdifferent thanSerialParam(), the default) and length offilesis larger than one, import is performed in parallel on a per-file basis. If data is to be imported from a single file (i.e., length offilesis one), parsing of the imported file is performed in parallel. See alsoBiocParallel::SerialParam()for information on available parallel processing setup options.- format
for
spectraVariableMapping():character(1)defining the format to be used. Currently onlyformat = "mgf"is supported.- x
for
export(): an instance ofSpectra::Spectra()class with the data that should be exported.- file
character(1)with the (full) file name to which the data should be exported.- exportTitle
logical(1)whether the TITLE field should be included in the exported MGF file. IfTRUE(the default) aspectraVariablecalled"TITLE"will be used, if no such variable is present either thespectraNames(object)will be used or, if they are empty, a title will be generated including the MS level, retention time and acquisition number of the spectrum.
Examples
library(BiocParallel)
#' Getting the file names of all example MGF files from MsBackendMgf
fls <- dir(system.file("extdata", package = "MsBackendMgf"),
full.names = TRUE, pattern = "^spectra(.*).mgf$")
## Create an MsBackendMgf backend and import data from test mgf files.
be <- backendInitialize(MsBackendMgf(), fls)
#> Start data import from 4 files ...
#> done
be
#> MsBackendMgf with 10 spectra
#> msLevel rtime scanIndex
#> <integer> <numeric> <integer>
#> 1 2 1028.00 NA
#> 2 2 1117.00 NA
#> 3 2 1127.00 NA
#> 4 2 2678.94 NA
#> 5 2 2373.51 NA
#> 6 2 2511.03 NA
#> 7 2 NA NA
#> 8 2 162.07 NA
#> 9 2 1028.00 NA
#> 10 2 1028.00 NA
#> ... 20 more variables/columns.
be$msLevel
#> [1] 2 2 2 2 2 2 2 2 2 2
be$intensity
#> NumericList of length 10
#> [[1]] 753.738 385.376 315.441 413.206 ... 3038.73 2016.43 1146.04 704.175
#> [[2]] 1228.93 1424.66 1550.9 1455.45 ... 7380.41 4960.92 5743.83 1780.76
#> [[3]] 1340.44 1714.76 1938.82 1450.36 2019 ... 5323.02 2265.43 4768.14 1532.12
#> [[4]] 81011.57 4123.349 4006.9321 66933.17 ... 22042.248 18096.48 12666.438
#> [[5]] 14.1766004562378 18.5806427001953 ... 22.7096385955811 14.864013671875
#> [[6]] 1748.57495117188 8689.9951171875 ... 2907.08422851562 2663.30908203125
#> [[7]] 65.219513 178.758606 13.01786 119.898499 ... 22.05921 30.57095 14.11111
#> [[8]] numeric(0)
#> [[9]] 753.738 385.376 315.441 413.206 ... 3038.73 2016.43 1146.04 704.175
#> [[10]] 753.738 385.376 315.441 413.206 ... 3038.73 2016.43 1146.04 704.175
be$mz
#> NumericList of length 10
#> [[1]] 102.0548 103.00494 103.03531 ... 1388.58691 1405.59729 1406.57666
#> [[2]] 101.07074 102.05486 103.00227 ... 1331.56726 1348.58496 1349.59241
#> [[3]] 102.05556 103.00014 115.05058 ... 1333.599 1334.61304 1335.64368
#> [[4]] 101.07122 109.68925 115.86999 120.0811 ... 1260.6073 1261.614 1272.6572
#> [[5]] 130.164459228516 144.150299072266 ... 1019.23852539062 1020.52404785156
#> [[6]] 110.070594787598 120.080627441406 ... 887.756652832031 998.447387695312
#> [[7]] 51.022404 57.033543 57.060638 ... 636.130188 660.481445 753.358521
#> [[8]] numeric(0)
#> [[9]] 102.0548 103.00494 103.03531 ... 1388.58691 1405.59729 1406.57666
#> [[10]] 102.0548 103.00494 103.03531 ... 1388.58691 1405.59729 1406.57666
## The spectra variables that are available; note that not all of them
## have been imported from the MGF files.
spectraVariables(be)
#> [1] "msLevel" "rtime"
#> [3] "acquisitionNum" "scanIndex"
#> [5] "mz" "intensity"
#> [7] "dataStorage" "dataOrigin"
#> [9] "centroided" "smoothed"
#> [11] "polarity" "precScanNum"
#> [13] "precursorMz" "precursorIntensity"
#> [15] "precursorCharge" "collisionEnergy"
#> [17] "isolationWindowLowerMz" "isolationWindowTargetMz"
#> [19] "isolationWindowUpperMz" "TITLE"
#> [21] "RAWFILE" "CLUSTER_ID"
#> [23] "MSLEVEL"
## The variable "TITLE" represents the title of the spectrum defined in the
## MGF file
be$TITLE
#> [1] "File193 Spectrum1719 scans: 2162"
#> [2] "File193 Spectrum1944 scans: 2406"
#> [3] "File193 Spectrum1968 scans: 2432"
#> [4] "mzspec:PXD004732:01650b_BC2-TUM_first_pool_53_01_01-3xHCD-1h-R2:scan:41840:WNQLQAFWGTGK/2"
#> [5] "mzspec:PXD002084:TCGA-AA-A01D-01A-23_W_VU_20121106_A0218_5I_R_FR15:scan:5209:DLTDYLMK/2"
#> [6] "mzspec:MSV000080679:j11962_C1orf144:scan:10671:DLTDYLMK/2"
#> [7] "CCMSLIB00000840351"
#> [8] "blank_2-A,1_01_29559.812.812.1"
#> [9] "File193 Spectrum1719 scans: 2162"
#> [10] "File193 Spectrum1719 scans: 2162"
## The default mapping of MGF fields to spectra variables is provided by
## the spectraVariableMapping function
spectraVariableMapping(MsBackendMgf())
#> rtime acquisitionNum precursorMz precursorIntensity
#> "RTINSECONDS" "SCANS" "PEPMASS" "PEPMASSINT"
#> precursorCharge
#> "CHARGE"
## We can provide our own mapping e.g. to map the MGF field "TITLE" to a
## variable named "spectrumName":
map <- c(spectrumName = "TITLE", spectraVariableMapping(MsBackendMgf()))
map
#> spectrumName rtime acquisitionNum precursorMz
#> "TITLE" "RTINSECONDS" "SCANS" "PEPMASS"
#> precursorIntensity precursorCharge
#> "PEPMASSINT" "CHARGE"
## We can then pass this mapping with parameter `mapping` to the
## backendInitialize method:
be <- backendInitialize(MsBackendMgf(), fls, mapping = map)
#> Start data import from 4 files ...
#> done
## The title is now available as variable named spectrumName
be$spectrumName
#> [1] "File193 Spectrum1719 scans: 2162"
#> [2] "File193 Spectrum1944 scans: 2406"
#> [3] "File193 Spectrum1968 scans: 2432"
#> [4] "mzspec:PXD004732:01650b_BC2-TUM_first_pool_53_01_01-3xHCD-1h-R2:scan:41840:WNQLQAFWGTGK/2"
#> [5] "mzspec:PXD002084:TCGA-AA-A01D-01A-23_W_VU_20121106_A0218_5I_R_FR15:scan:5209:DLTDYLMK/2"
#> [6] "mzspec:MSV000080679:j11962_C1orf144:scan:10671:DLTDYLMK/2"
#> [7] "CCMSLIB00000840351"
#> [8] "blank_2-A,1_01_29559.812.812.1"
#> [9] "File193 Spectrum1719 scans: 2162"
#> [10] "File193 Spectrum1719 scans: 2162"
## Next we create a Spectra object with this data
sps <- Spectra(be)
## We can use the 'MsBackendMgf' also to export spectra data in mgf format.
out_file <- tempfile()
export(sps, backend = MsBackendMgf(), file = out_file, map = map)
## The first 20 lines of the generated file:
readLines(out_file, n = 20)
#> [1] "BEGIN IONS"
#> [2] "msLevel=2"
#> [3] "RTINSECONDS=1028"
#> [4] "SCANS=2162"
#> [5] "centroided=TRUE"
#> [6] "PEPMASS=816.33826"
#> [7] "CHARGE=2+"
#> [8] "TITLE=File193 Spectrum1719 scans: 2162"
#> [9] "102.0548 753.738"
#> [10] "103.00494 385.376"
#> [11] "103.03531 315.441"
#> [12] "115.05001 413.206"
#> [13] "115.08686 588.273"
#> [14] "120.08063 800.016"
#> [15] "124.10555 526.761"
#> [16] "124.20652 326.013"
#> [17] "1369.57385 1485.17"
#> [18] "1370.57495 1280.2"
#> [19] "1387.59021 3038.73"
#> [20] "1388.58691 2016.43"
## Next we add a new spectra variable to each spectrum
sps$spectrum_idx <- seq_along(sps)
## This new spectra variable will also be exported to the mgf file:
export(sps, backend = MsBackendMgf(), file = out_file, map = map)
readLines(out_file, n = 20)
#> [1] "BEGIN IONS"
#> [2] "msLevel=2"
#> [3] "RTINSECONDS=1028"
#> [4] "SCANS=2162"
#> [5] "centroided=TRUE"
#> [6] "PEPMASS=816.33826"
#> [7] "CHARGE=2+"
#> [8] "TITLE=File193 Spectrum1719 scans: 2162"
#> [9] "spectrum_idx=1"
#> [10] "102.0548 753.738"
#> [11] "103.00494 385.376"
#> [12] "103.03531 315.441"
#> [13] "115.05001 413.206"
#> [14] "115.08686 588.273"
#> [15] "120.08063 800.016"
#> [16] "124.10555 526.761"
#> [17] "124.20652 326.013"
#> [18] "1369.57385 1485.17"
#> [19] "1370.57495 1280.2"
#> [20] "1387.59021 3038.73"
####
## Annotated MGF
## An example of a supported annotated MGF file
fl <- system.file("extdata", "xfiora.mgf", package = "MsBackendMgf")
## Lines with peak data start with a numeric and information is
## separated by a whitespace. The first two elements are the peak's m/z
## and intensity while any additional information is considered as
## annotation. Information for each peak is provided in one line.
readLines(fl)
#> [1] "BEGIN IONS"
#> [2] "TITLE=PC(PGF1alpha/22:6(4Z,7Z,10Z,13Z,16Z,19Z))"
#> [3] "SMILES=CCCCCC@@HO"
#> [4] "PRECURSORTYPE=[M+H]+"
#> [5] "COLLISIONENERGY=10.0"
#> [6] "INSTRUMENTTYPE=HCD"
#> [7] "COMMENT=\"In silico generated spectrum by Fiora OS v0.1.0\""
#> [8] "906.5854755900899 0.24612045288085938 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [9] "57.06987670808999 0.0012485487386584282 CCCC//[M-H]+"
#> [10] "71.08552677208999 0.0015523125184699893 CCCCC//[M-H]+"
#> [11] "100.08826642409 0.0031058108434081078 CCCCC[CH]O//[M-H]+"
#> [12] "804.48101052209 0.003057875670492649 C=C[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+"
#> [13] "888.575459486 0.002360690850764513 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M]+"
#> [14] "887.56708587409 0.02812790870666504 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [15] "790.4653604580899 0.0010008384706452489 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [16] "887.56708587409 0.002026958856731653 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [17] "19.01784113609 0.009557841811329126 O//[M+H]+"
#> [18] "887.56708587409 0.0032752526458352804 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [19] "678.4129309620901 0.0013166849967092276 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [20] "311.25807140009 0.0020137864630669355 CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M-H]+"
#> [21] "339.25298602008996 0.03245394676923752 CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+"
#> [22] "568.33976602209 0.14936257898807526 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [23] "357.26355070408994 0.003117065876722336 CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M+H]+"
#> [24] "550.32920133809 0.012815228663384914 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [25] "578.3457939059999 0.002960008103400469 CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M]+"
#> [26] "577.33742029409 0.030111582949757576 CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+"
#> [27] "329.24750671609 0.002531866542994976 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)O//[M+H]+"
#> [28] "725.5350810960899 0.0012065907940268517 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@@HCOC(=O)CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M+H]+"
#> [29] "724.527804644 0.0018646189710125327 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@@HCOC(=O)CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M]+"
#> [30] "723.51943103209 0.038313210010528564 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@@HCOC(=O)CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M-H]+"
#> [31] "183.06604455800002 0.005070459563285112 CN+(C)CCOP(=O)([O-])O//[M]+"
#> [32] "15.995463199909999 0.004359378479421139 [O-]//[M]+"
#> [33] "104.10699048808999 0.0013647250598296523 CN+(C)CCO//[M]+"
#> [34] "819.4817733339099 0.001787053421139717 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])O//[M]+"
#> [35] "88.11207586808999 0.00103498506359756 CCN+(C)C//[M]+"
#> [36] "87.10370225617999 0.008224652148783207 CCN+(C)C//[M-H]+"
#> [37] "86.09642580408999 0.011802508495748043 CCN+(C)C//[M-2H]+"
#> [38] "85.08805219217999 0.0019315838580951095 CCN+(C)C//[M-3H]+"
#> [39] "73.08805219217999 0.002003903966397047 CN+(C)C//[M-H]+"
#> [40] "846.50469985 0.003967077471315861 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCC//[M-H]+"
#> [41] "60.08022716018 0.002686966210603714 CN+C//[M+H]+"
#> [42] "58.06457709618 0.0016727085458114743 CN+C//[M-H]+"
#> [43] "596.35581001009 0.055958326905965805 CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M+H]+"
#> [44] "311.23694203209004 0.015817463397979736 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC=O//[M-H]+"
#> [45] "283.24202741209 0.0027298536151647568 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [46] "255.21072728408998 0.0011316784657537937 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [47] "662.3663746940899 0.0015134515706449747 CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M-3H]+"
#> [48] "241.19507722008998 0.0017022188985720277 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [49] "676.38202475809 0.0012113102711737156 C=CCCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [50] "674.3663746940899 0.0030237638857215643 C=CCCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [51] "229.19507722008998 0.004923875909298658 C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [52] "690.39767482209 0.007068068254739046 C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [53] "688.38202475809 0.0011182071175426245 C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [54] "217.19507722008998 0.004412529990077019 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M+H]+"
#> [55] "215.17942715609 0.00425428943708539 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [56] "213.16377709209 0.0066286781802773476 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [57] "702.3976748220899 0.005614385008811951 CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [58] "201.16377709209 0.004419034346938133 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [59] "718.4289749500899 0.002718859352171421 C=CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [60] "716.41332488609 0.002932032337412238 C=CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [61] "714.3976748220899 0.00470602186396718 C=CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [62] "189.16377709209 0.006993195042014122 C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [63] "187.14812702809 0.0015772052574902773 C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [64] "730.42897495009 0.006089580710977316 C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [65] "728.41332488609 0.0011209301883354783 C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [66] "177.16377709209 0.0047977156937122345 C=CC/C=C\\C/C=C\\C/C=C\\CC//[M+H]+"
#> [67] "175.14812702809 0.0039370497688651085 C=CC/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [68] "173.13247696409 0.006436163559556007 C=CC/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [69] "742.4289749500899 0.0065302494913339615 CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [70] "161.13247696409 0.005028888117522001 CC/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [71] "758.4602750780899 0.0027850852347910404 C=CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [72] "756.44462501409 0.0030861366540193558 C=CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [73] "754.4289749500899 0.004762527532875538 C=CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [74] "149.13247696409 0.007314636372029781 C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [75] "147.11682690009 0.0016508938279002905 C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [76] "770.46027507809 0.006089580710977316 C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [77] "768.44462501409 0.0011209301883354783 C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [78] "137.13247696409 0.0047977156937122345 C=CC/C=C\\C/C=C\\CC//[M+H]+"
#> [79] "135.11682690009 0.0039370497688651085 C=CC/C=C\\C/C=C\\CC//[M-H]+"
#> [80] "133.10117683609 0.006436163559556007 C=CC/C=C\\C/C=C\\CC//[M-3H]+"
#> [81] "782.4602750780899 0.0065302494913339615 CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [82] "121.10117683608999 0.005028888117522001 CC/C=C\\C/C=C\\CC//[M-3H]+"
#> [83] "798.4915752060899 0.0027850852347910404 C=CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [84] "796.47592514209 0.0030861366540193558 C=CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [85] "794.4602750780899 0.004762527532875538 C=CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [86] "109.10117683608999 0.007314636372029781 C/C=C\\C/C=C\\CC//[M-H]+"
#> [87] "107.08552677208999 0.0016508938279002905 C/C=C\\C/C=C\\CC//[M-3H]+"
#> [88] "810.49157520609 0.006118484307080507 C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [89] "808.47592514209 0.0010935019236057997 C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [90] "97.10117683608999 0.00479193776845932 C=CC/C=C\\CC//[M+H]+"
#> [91] "95.08552677208999 0.00393778458237648 C=CC/C=C\\CC//[M-H]+"
#> [92] "93.06987670808999 0.00646106107160449 C=CC/C=C\\CC//[M-3H]+"
#> [93] "822.4915752060899 0.007105632219463587 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [94] "81.06987670808999 0.0054127830080688 CC/C=C\\CC//[M-3H]+"
#> [95] "838.5228753340899 0.0024260678328573704 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [96] "836.50722527009 0.003049242775887251 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [97] "834.4915752060899 0.004425586201250553 C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [98] "69.06987670808999 0.008552799001336098 C/C=C\\CC//[M-H]+"
#> [99] "67.05422664409 0.0017731321277096868 C/C=C\\CC//[M-3H]+"
#> [100] "850.52287533409 0.00296195806004107 C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [101] "57.06987670808999 0.002908135997131467 C=CCC//[M+H]+"
#> [102] "55.054226644089994 0.0025195078924298286 C=CCC//[M-H]+"
#> [103] "53.038576580089995 0.0017213564133271575 C=CCC//[M-3H]+"
#> [104] "862.5228753340899 0.0011330428533256054 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [105] "END IONS"
## Importing the data using an `MsBackendAnnotatedMgf`
ba <- backendInitialize(MsBackendAnnotatedMgf(), fl)
#> Start data import from 1 files ...
#> done
ba
#> MsBackendAnnotatedMgf with 1 spectra
#> msLevel rtime scanIndex
#> <integer> <numeric> <integer>
#> 1 2 NA NA
#> ... 23 more variables/columns.
## An additional peaks variable is available.
peaksVariables(ba)
#> [1] "mz" "intensity" "V1"
ba$V1
#> [[1]]
#> [1] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [2] "CCCC//[M-H]+"
#> [3] "CCCCC//[M-H]+"
#> [4] "CCCCC[CH]O//[M-H]+"
#> [5] "C=C[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+"
#> [6] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M]+"
#> [7] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [8] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [9] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [10] "O//[M+H]+"
#> [11] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [12] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [13] "CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M-H]+"
#> [14] "CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+"
#> [15] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [16] "CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M+H]+"
#> [17] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [18] "CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M]+"
#> [19] "CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+"
#> [20] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)O//[M+H]+"
#> [21] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@@HCOC(=O)CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M+H]+"
#> [22] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@@HCOC(=O)CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M]+"
#> [23] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@@HCOC(=O)CCCCCC[C@@h]1C@@HC@HC[C@@h]1O//[M-H]+"
#> [24] "CN+(C)CCOP(=O)([O-])O//[M]+"
#> [25] "[O-]//[M]+"
#> [26] "CN+(C)CCO//[M]+"
#> [27] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])O//[M]+"
#> [28] "CCN+(C)C//[M]+"
#> [29] "CCN+(C)C//[M-H]+"
#> [30] "CCN+(C)C//[M-2H]+"
#> [31] "CCN+(C)C//[M-3H]+"
#> [32] "CN+(C)C//[M-H]+"
#> [33] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCC//[M-H]+"
#> [34] "CN+C//[M+H]+"
#> [35] "CN+C//[M-H]+"
#> [36] "CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M+H]+"
#> [37] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC=O//[M-H]+"
#> [38] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [39] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [40] "CCCCCC@H/C=C/[C@@h]1C@@HC@@HC[C@H]1O//[M-3H]+"
#> [41] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [42] "C=CCCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [43] "C=CCCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [44] "C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [45] "C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [46] "C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [47] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M+H]+"
#> [48] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [49] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [50] "CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [51] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [52] "C=CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [53] "C=CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [54] "C=CC/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [55] "C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [56] "C/C=C\\C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [57] "C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [58] "C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [59] "C=CC/C=C\\C/C=C\\C/C=C\\CC//[M+H]+"
#> [60] "C=CC/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [61] "C=CC/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [62] "CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [63] "CC/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [64] "C=CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [65] "C=CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [66] "C=CC/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [67] "C/C=C\\C/C=C\\C/C=C\\CC//[M-H]+"
#> [68] "C/C=C\\C/C=C\\C/C=C\\CC//[M-3H]+"
#> [69] "C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [70] "C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [71] "C=CC/C=C\\C/C=C\\CC//[M+H]+"
#> [72] "C=CC/C=C\\C/C=C\\CC//[M-H]+"
#> [73] "C=CC/C=C\\C/C=C\\CC//[M-3H]+"
#> [74] "CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [75] "CC/C=C\\C/C=C\\CC//[M-3H]+"
#> [76] "C=CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [77] "C=CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [78] "C=CC/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [79] "C/C=C\\C/C=C\\CC//[M-H]+"
#> [80] "C/C=C\\C/C=C\\CC//[M-3H]+"
#> [81] "C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [82] "C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [83] "C=CC/C=C\\CC//[M+H]+"
#> [84] "C=CC/C=C\\CC//[M-H]+"
#> [85] "C=CC/C=C\\CC//[M-3H]+"
#> [86] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [87] "CC/C=C\\CC//[M-3H]+"
#> [88] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+"
#> [89] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [90] "C=CC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#> [91] "C/C=C\\CC//[M-H]+"
#> [92] "C/C=C\\CC//[M-3H]+"
#> [93] "C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-H]+"
#> [94] "C=CCC//[M+H]+"
#> [95] "C=CCC//[M-H]+"
#> [96] "C=CCC//[M-3H]+"
#> [97] "CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M-3H]+"
#>
## The length of such peaks variables is the same as the length of the
## m/z or intensity values, i.e. each peak has one value (with the value
## being `NA` if missing).
length(ba$V1[[1L]])
#> [1] 97
length(ba$mz[[1L]])
#> [1] 97
## Extracting the peaks data from a `Spectra` with a `MsBackendAnnotatedMgf`
s <- Spectra(ba)
pd <- peaksData(s, peaksVariables(ba))[[1L]]
head(pd)
#> mz intensity
#> 1 15.99546 0.004359378
#> 2 19.01784 0.009557842
#> 3 53.03858 0.001721356
#> 4 55.05423 0.002519508
#> 5 57.06988 0.001248549
#> 6 57.06988 0.002908136
#> V1
#> 1 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M+H]+
#> 2 CCCC//[M-H]+
#> 3 CCCCC//[M-H]+
#> 4 CCCCC[CH]O//[M-H]+
#> 5 C=C[C@@h]1C@@HC@@HC[C@H]1O//[M-H]+
#> 6 CC/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\C/C=C\\CCC(=O)OC@HCOP(=O)([O-])OCCN+(C)C//[M]+
class(pd)
#> [1] "data.frame"