MS data backend for msp files — MsBackendMsp • MsBackendMsp

The MsBackendMsp class supports import of MS/MS spectra data from files in NIST MSP file format. MsBackendMsp extends the MsBackendDataFrame() backend directly and supports thus the applyProcessing() function to make data manipulations persistent.

New objects are created with the MsBackendMsp() function. The backendInitialize() method has to be subsequently called to initialize the object and import MS/MS data from (one or more) msp files.

The MsBackendMsp backend provides an export() method that allows to export the data from the Spectra object (parameter x) to a file in MSP format.

Parameters to this function are:

x: the Spectra object that should be exported.
file: character(1) with the desired file name.
mapping: named character providing the mapping between spectra variables and MSP data fields. Defaults to mapping = spectraVariableMapping(MsBackendMsp()).
allVariables: logical(1) whether all spectra variables in x should be exported or only those defined with mapping.
exportName: logical(1) whether a NAME field should always be exported even if not provided in x.

See the package vignette for details and examples.

The spectraVariableMapping() function allows to provide the mapping between spectra variable names (i.e. the names that will be used for the spectra variables in the Spectra() object) and the data field names of the MSP file. Parameter format allows to select pre-defined mappings. Currently supported mapping flavors are:

format = "msp": default MSP field names. Should work with standard NIST MSP files or MSP files exported from MS-DIAL.
format = "mona": MSP file format from MoNA including LipidBlast.

Usage

# S4 method for class 'MsBackendMsp'
backendInitialize(
  object,
  file,
  mapping = spectraVariableMapping(object),
  ...,
  BPPARAM = SerialParam()
)

MsBackendMsp()

# S4 method for class 'MsBackendMsp'
spectraVariableMapping(object, format = c("msp", "mona"))

# S4 method for class 'MsBackendMsp'
export(
  object,
  x,
  file = tempfile(),
  mapping = spectraVariableMapping(MsBackendMsp()),
  allVariables = TRUE,
  exportName = TRUE,
  ...
)

Arguments

object: Instance of MsBackendMsp class.
file: character with the (full) file name(s) of the msp file(s) from which MS/MS data should be imported or exported.
mapping: named character vector to rename MSP fields to spectra variables (see spectraVariableMapping()). This allows to correctly import also custom fields or data from files with different MSP flavors.
...: Currently ignored.
BPPARAM: Parameter object defining the parallel processing setup to import data in parallel. Defaults to BPPARAM = SerialParam(). See bpparam() for more information. Parallel processing would make most sense for import from a large set of individual MSP files, but could also improve performance for import from a (very large) single MSP file.
format: For spectraVariableMapping(): character(1) specifying for which MSP flavour the mapping should be returned. Currently supported are: format = "msp" (generic MSP format, for example for MS-DIAL MSP files) and format = "mona" (MSP files in MoNA flavour).
x: For export(): a Spectra() object that should be exported to the specified MSP file.
allVariables: logical(1) whether all spectra variables in x should be exported or only those defined with mapping.
exportName: logical(1) whether a NAME field should always be exported even if not provided in x.

Value

MsBackendMsp() and backendInitialize() return an instance of a MsBackendMsp class. spectraVariableMapping() a named character vector with the mapping between spectra variables and MSP data fields.

Note

Format requirements/assumptions of MSP files:

Comment lines are expected to start with a #.
Multiple spectra within the same MSP file are separated by an empty line.
The first n lines of a spectrum entry represent metadata.
Metadata is provided as "name: value" pairs (i.e. name and value separated by a ":").
One line per mass peak, with values separated by a whitespace or tabulator.
Each line is expected to contain at least the m/z and intensity values (in that order) of a peak. Additional values are currently ignored.

Author

Steffen Neumann, Michael Witting, Laurent Gatto and Johannes Rainer

Examples


## Import spectra from a MSP file from LipidBlast
f <- system.file("extdata", "small-export-LipidBlast.msp",
    package = "MsBackendMsp")
be <- backendInitialize(MsBackendMsp(), f)
be
#> MsBackendMsp with 5 spectra
#>     msLevel     rtime scanIndex
#>   <integer> <numeric> <integer>
#> 1         2        NA        NA
#> 2         2        NA        NA
#> 3         2        NA        NA
#> 4         2        NA        NA
#> 5         2        NA        NA
#>  ... 32 more variables/columns.

be$msLevel
#> [1] 2 2 2 2 2
be$intensity
#> NumericList of length 5
#> [[1]] 80.08008 100
#> [[2]] 80.08008 100
#> [[3]] 80.08008 100
#> [[4]] 30.03003 50.05005 50.05005 50.05005 ... 70.07007 50.05005 50.05005 100
#> [[5]] 30.03003 50.05005 50.05005 50.05005 ... 70.07007 50.05005 50.05005 100
be$mz
#> NumericList of length 5
#> [[1]] 85.02841 232.1543
#> [[2]] 85.02841 246.17
#> [[3]] 85.02841 260.1856
#> [[4]] 152.9958 227.2016 283.2643 327.2329 ... 691.4344 703.5283 1451.996
#> [[5]] 152.9958 253.2173 255.233 281.2486 ... 673.4814 721.4814 1451.996

## precursor m/z are however all missing
be$precursorMz
#> [1] NA NA NA NA NA

## Default spectra variable mapping
spectraVariableMapping(MsBackendMsp())
#>            name       accession         formula        inchikey          adduct 
#>          "NAME"           "DB#"       "FORMULA"      "INCHIKEY" "PRECURSORTYPE" 
#>       exactmass           rtime     precursorMz          adduct          smiles 
#>     "EXACTMASS" "RETENTIONTIME"   "PRECURSORMZ" "PRECURSORTYPE"        "SMILES" 
#>           inchi        polarity      instrument 
#>         "INCHI"       "IONMODE"    "INSTRUMENT" 

## In fact, to read MSP files in "LipidBlast flavour" (same as MoNA) we
## should use a different spectra variable mapping
spectraVariableMapping(MsBackendMsp(), "mona")
#>                  name               synonym             accession 
#>                "Name"               "Synon"                 "DB#" 
#>              inchikey                adduct           precursorMz 
#>            "InChIKey"      "Precursor_type"         "PrecursorMZ" 
#>              polarity               formula             exactmass 
#>            "Ion_mode"             "Formula"           "ExactMass" 
#> collision_energy_text               msLevel            instrument 
#>    "Collision_energy"       "Spectrum_type"          "Instrument" 
#>       instrument_type 
#>     "Instrument_type" 

## Importing the data with this will correctly retrieve data
be <- backendInitialize(MsBackendMsp(), f,
    mapping = spectraVariableMapping(MsBackendMsp(), "mona"))
be$precursorMz
#> [1]  232.1543  246.1700  260.1856 1451.9962 1451.9962

## Other fields are also correctly mapped, but might need to be converted
## to e.g. numeric, such as "exactmass"
be$exactmass
#> [1] "232.1543346040907"  "246.16998466809073" "260.18563473209076"
#> [4] "1453.003526472"     "1453.003526472"    

be$exactmass <- as.numeric(be$exactmass)

be$adduct
#> [1] "[M]+"   "[M]+"   "[M]+"   "[M-H]-" "[M-H]-"
be$formula
#> [1] "[C11H22NO4]+" "[C12H24NO4]+" "[C13H26NO4]+" "C81H146O17P2" "C81H146O17P2"

## Exporting Spectra objects in MSP format.

sps <- Spectra(be)
export(MsBackendMsp(), sps, file = stdout())
#> NAME: ACar 4:0
#> msLevel: MS2
#> IONMODE: Positive
#> PRECURSORMZ: 232.15433
#> Comments: "SMILES=CCCC(=O)OC(CC(O)=O)C[N+](C)(C)C" "compound class=ACar" "computed SMILES=O=C(O)CC(OC(=O)CCC)C[N+](C)(C)C" "computed InChI=InChI=1S/C11H21NO4/c1-5-6-11(15)16-9(7-10(13)14)8-12(2,3)4/h9H,5-8H2,1-4H3/p+1" "retention time=0.51" "collision energy spread=15 V" "author=Tobias Kind, Hiroshi Tsugawa" "computed mass accuracy=2.3431646471704717" "computed mass error=5.439758187435473E-4" "SPLASH=splash10-001r-7090000000-aa12589a2481560ea0d5" "submitter=Tobias Kind (University of California, Davis)" "MoNA Rating=3.6363636363636367"
#> MW: 232
#> Num.Peaks: 2
#> DB#: LipidBlast000001
#> PRECURSORTYPE: [M]+
#> collision_energy_text: 45 V
#> EXACTMASS: 232.154334604091
#> FORMULA: [C11H22NO4]+
#> INCHIKEY: QWYFHHGCZUCMBN-UHFFFAOYSA-O
#> INSTRUMENT: SCIEX 5600
#> instrument_type: in-silico QTOF
#> synonym: [M]+
#> synonym: $:00in-source
#> Num Peaks: 2
#> 85.02841 80.08008
#> 232.1543 100
#> 
#> NAME: ACar 5:0
#> msLevel: MS2
#> IONMODE: Positive
#> PRECURSORMZ: 246.16998
#> Comments: "SMILES=CCCCC(=O)OC(CC(O)=O)C[N+](C)(C)C" "compound class=ACar" "computed SMILES=O=C(O)CC(OC(=O)CCCC)C[N+](C)(C)C" "computed InChI=InChI=1S/C12H23NO4/c1-5-6-7-12(16)17-10(8-11(14)15)9-13(2,3)4/h10H,5-9H2,1-4H3/p+1" "retention time=0.68" "collision energy spread=15 V" "author=Tobias Kind, Hiroshi Tsugawa" "computed mass accuracy=2.209496944908765" "computed mass error=5.439118187382519E-4" "SPLASH=splash10-000b-7090000000-2b596f4df94dfefba50b" "submitter=Tobias Kind (University of California, Davis)" "MoNA Rating=3.6363636363636367"
#> MW: 246
#> Num.Peaks: 2
#> DB#: LipidBlast000002
#> PRECURSORTYPE: [M]+
#> collision_energy_text: 45 V
#> EXACTMASS: 246.169984668091
#> FORMULA: [C12H24NO4]+
#> INCHIKEY: VSNFQQXVMPSASB-UHFFFAOYSA-O
#> INSTRUMENT: SCIEX 5600
#> instrument_type: in-silico QTOF
#> synonym: [M]+
#> synonym: $:00in-source
#> Num Peaks: 2
#> 85.02841 80.08008
#> 246.17 100
#> 
#> NAME: ACar 6:0
#> msLevel: MS2
#> IONMODE: Positive
#> PRECURSORMZ: 260.18563
#> Comments: "SMILES=CCCCCC(=O)OC(CC(O)=O)C[N+](C)(C)C" "compound class=ACar" "computed SMILES=O=C(O)CC(OC(=O)CCCCC)C[N+](C)(C)C" "computed InChI=InChI=1S/C13H25NO4/c1-5-6-7-8-13(17)18-11(9-12(15)16)10-14(2,3)4/h11H,5-10H2,1-4H3/p+1" "retention time=0.86" "collision energy spread=15 V" "author=Tobias Kind, Hiroshi Tsugawa" "computed mass accuracy=2.0902300356715053" "computed mass error=5.438478186761131E-4" "SPLASH=splash10-03dr-7090000000-a9ec485bc43949b4b278" "submitter=Tobias Kind (University of California, Davis)" "MoNA Rating=3.6363636363636367"
#> MW: 260
#> Num.Peaks: 2
#> DB#: LipidBlast000003
#> PRECURSORTYPE: [M]+
#> collision_energy_text: 45 V
#> EXACTMASS: 260.185634732091
#> FORMULA: [C13H26NO4]+
#> INCHIKEY: VVPRQWTYSNDTEA-UHFFFAOYSA-O
#> INSTRUMENT: SCIEX 5600
#> instrument_type: in-silico QTOF
#> synonym: [M]+
#> synonym: $:00in-source
#> Num Peaks: 2
#> 85.02841 80.08008
#> 260.1856 100
#> 
#> NAME: CL 72:6
#> msLevel: MS2
#> IONMODE: Negative
#> PRECURSORMZ: 1451.99625
#> Comments: "SMILES=CCCCCCCCCCCCCCCCCC(=O)OCC(COP(O)(=O)OCC(O)COP(O)(=O)OCC(COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CC)OC(=O)CCCCCCCCCCCCC)OC(=O)CCCCCCCCCCCCCCCCC" "compound class=CL" "computed SMILES=O=C(OCC(OC(=O)CCCCCCCCCCCCC)COP(=O)(O)OCC(O)COP(=O)(O)OCC(OC(=O)CCCCCCCCCCCCCCCCC)COC(=O)CCCCCCCCCCCCCCCCC)CCC=CCC=CCC=CCC=CCC=CCC=CCC" "computed InChI=InChI=1S/C81H146O17P2/c1-5-9-13-17-21-25-29-32-35-36-37-38-41-43-47-50-54-58-62-66-79(84)91-71-76(97-80(85)67-63-59-55-51-45-28-24-20-16-12-8-4)73-95-99(87,88)93-69-75(82)70-94-100(89,90)96-74-77(98-81(86)68-64-60-56-52-48-44-40-34-31-27-23-19-15-11-7-3)72-92-78(83)65-61-57-53-49-46-42-39-33-30-26-22-18-14-10-6-2/h9,13,21,25,32,35,37-38,43,47,54,58,75-77,82H,5-8,10-12,14-20,22-24,26-31,33-34,36,39-42,44-46,48-53,55-57,59-74H2,1-4H3,(H,87,88)(H,89,90)/b13-9-,25-21-,35-32-,38-37-,47-43-,58-54-" "retention time=11.91" "collision energy spread=15 V" "author=Tobias Kind, Hiroshi Tsugawa" "computed mass accuracy=3.2506971738511424E-4" "computed mass error=-4.720000106317457E-7" "SPLASH=splash10-0w4i-0134901100-d27b9577a1230ec65177" "submitter=Tobias Kind (University of California, Davis)" "MoNA Rating=4.5"
#> MW: 1453
#> Num.Peaks: 10
#> DB#: LipidBlast395475
#> PRECURSORTYPE: [M-H]-
#> collision_energy_text: 45 V
#> EXACTMASS: 1453.003526472
#> FORMULA: C81H146O17P2
#> INCHIKEY: KWABUIIFXPUAEH-OXNFOSRESA-N
#> INSTRUMENT: SCIEX 5600
#> instrument_type: in-silico QTOF
#> synonym: CL 14:0-22:6-18:0-18:0
#> synonym: $:00in-source
#> Num Peaks: 10
#> 152.9958 30.03003
#> 227.2016 50.05005
#> 283.2643 50.05005
#> 327.2329 50.05005
#> 363.1942 70.07007
#> 419.2568 70.07007
#> 463.2255 70.07007
#> 691.4344 50.05005
#> 703.5283 50.05005
#> 1451.996 100
#> 
#> NAME: CL 72:6
#> msLevel: MS2
#> IONMODE: Negative
#> PRECURSORMZ: 1451.99625
#> Comments: "SMILES=CCCCCCCCCCCCCCCC(=O)OC(COC(=O)CCCCCCC\C=C/CCCCCCCC)COP(O)(=O)OCC(O)COP(O)(=O)OCC(COC(=O)CCCCCCCC\C=C/C\C=C/C\C=C/C\C=C/CC)OC(=O)CCCCCCC\C=C/CCCCCC" "compound class=CL" "computed SMILES=O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COP(=O)(O)OCC(O)COP(=O)(O)OCC(OC(=O)CCCCCCCC=CCCCCCC)COC(=O)CCCCCCCCC=CCC=CCC=CCC=CCC)CCCCCCCC=CCCCCCCCC" "computed InChI=InChI=1S/C81H146O17P2/c1-5-9-13-17-21-25-29-33-35-36-37-38-40-44-46-50-54-58-62-66-79(84)92-72-77(98-81(86)68-64-60-56-52-48-42-32-28-24-20-16-12-8-4)74-96-100(89,90)94-70-75(82)69-93-99(87,88)95-73-76(97-80(85)67-63-59-55-51-47-41-31-27-23-19-15-11-7-3)71-91-78(83)65-61-57-53-49-45-43-39-34-30-26-22-18-14-10-6-2/h9,13,21,25,28,32-35,37-39,75-77,82H,5-8,10-12,14-20,22-24,26-27,29-31,36,40-74H2,1-4H3,(H,87,88)(H,89,90)/b13-9-,25-21-,32-28-,35-33-,38-37-,39-34-" "retention time=11.65" "collision energy spread=15 V" "author=Tobias Kind, Hiroshi Tsugawa" "computed mass accuracy=3.2506971738511424E-4" "computed mass error=-4.720000106317457E-7" "SPLASH=splash10-0uyi-0157901100-d3b7dfa9dd7050026484" "submitter=Tobias Kind (University of California, Davis)" "MoNA Rating=4.5"
#> MW: 1453
#> Num.Peaks: 12
#> DB#: LipidBlast398514
#> PRECURSORTYPE: [M-H]-
#> collision_energy_text: 45 V
#> EXACTMASS: 1453.003526472
#> FORMULA: C81H146O17P2
#> INCHIKEY: WINXBODRGKNJDS-DUULZMMUSA-N
#> INSTRUMENT: SCIEX 5600
#> instrument_type: in-silico QTOF
#> synonym: CL 16:0-18:1-16:1-22:4
#> synonym: $:00in-source
#> Num Peaks: 12
#> 152.9958 30.03003
#> 253.2173 50.05005
#> 255.233 50.05005
#> 281.2486 50.05005
#> 331.2643 50.05005
#> 389.2098 70.07007
#> 391.2255 70.07007
#> 417.2411 70.07007
#> 467.2568 70.07007
#> 673.4814 50.05005
#> 721.4814 50.05005
#> 1451.996 100
#>