The readMsp() function imports the data from a file in MGF format reading
all specified fields and returning the data as a DataFrame().
Format constraints for 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.
Usage
readMsp(
f,
msLevel = 2L,
mapping = spectraVariableMapping(MsBackendMsp()),
BPPARAM = SerialParam(),
...
)Arguments
- f
character(1)with the path to an MSP file.- msLevel
numeric(1)with the MS level. Default is 2. This value will be reported as the spectra's MS level unless the source MSP file defines the MS level.- mapping
named
charactervector to rename MSP fields to spectra variables (seespectraVariableMapping()). This allows to correctly import also custom fields or data from files with different MSP flavors.- BPPARAM
parallel processing setup. See
bpparam()for more details.- ...
Additional parameters, currently ignored.
Value
A DataFrame with each row containing the data from one spectrum
in the MSP file. m/z and intensity values are available in columns "mz"
and "intensity" in a list representation.
Examples
f <- system.file("extdata", "minimona.msp", package = "MsBackendMsp")
readMsp(f)
#> DataFrame with 30 rows and 19 columns
#> Name Synon
#> <character> <list>
#> 1 Ritonavir $:00in-source
#> 2 Unknown $:00in-source
#> 3 Unknown $:00in-source
#> 4 Unknown $:00in-source
#> 5 Unknown $:00in-source
#> ... ... ...
#> 26 7-MAHPDA [DMED-FAHFA.. $:00 ms2,$:05 30V CID,$:07 In-Silico-Spect..,...
#> 27 8-MAHPDA [DMED-FAHFA.. $:00 ms2,$:05 30V CID,$:07 In-Silico-Spect..,...
#> 28 9-MAHPDA [DMED-FAHFA.. $:00 ms2,$:05 30V CID,$:07 In-Silico-Spect..,...
#> 29 10-MAHPDA [DMED-FAHF.. $:00 ms2,$:05 30V CID,$:07 In-Silico-Spect..,...
#> 30 11-MAHPDA [DMED-FAHF.. $:00 ms2,$:05 30V CID,$:07 In-Silico-Spect..,...
#> accession InChIKey Instrument_type Formula
#> <character> <character> <character> <character>
#> 1 MoNA000010 NCDNCNXCDXHOMX-XGKFQ.. Waters Synapt G2 C37H48N6O5S2
#> 2 MoNA000012 MXNRLFUSFKVQSK-QMMMG.. NA H2O
#> 3 MoNA000013 JFLIEFSWGNOPJJ-JTQLQ.. NA C13H16N2O4
#> 4 MoNA000014 MXNRLFUSFKVQSK-QMMMG.. NA C9H20N2O2
#> 5 MoNA000015 JFLIEFSWGNOPJJ-JTQLQ.. NA C13H16N2O4
#> ... ... ... ... ...
#> 26 MoNA011542 MQTXDUJVZFSMBT-UHFFF.. NA NA
#> 27 MoNA011543 CYZGZMTYUCCRMO-UHFFF.. NA NA
#> 28 MoNA011544 GREOXQBULJWSQV-UHFFF.. NA NA
#> 29 MoNA011545 GPDSFBGRMDEPAY-UHFFF.. NA NA
#> 30 MoNA011546 QGMGRNCZWXKENS-UHFFF.. NA NA
#> MW ExactMass Comments Num.Peaks
#> <character> <character> <character> <character>
#> 1 720 720.3127606360001 "computed SMILES=OC(.. 8
#> 2 18 18.010564684 "computed SMILES=O" .. 29
#> 3 264 264.111006992 "computed SMILES=O=C.. 21
#> 4 188 188.15247788 "computed SMILES=O=C.. 10
#> 5 264 264.111006992 "computed SMILES=O=C.. 18
#> ... ... ... ... ...
#> 26 NA NA "molecular weight=53.. 4
#> 27 NA NA "molecular weight=53.. 4
#> 28 NA NA "molecular weight=53.. 4
#> 29 NA NA "molecular weight=53.. 4
#> 30 NA NA "molecular weight=53.. 4
#> mz intensity Precursor_type
#> <NumericList> <NumericList> <character>
#> 1 140.054,171.096,197.075,... 18.018,18.018,31.031,... NA
#> 2 41.0418,42.0375,43.0201,... 2.036603,1.781709,0.795269,... [M+H]+
#> 3 41.0442,56.0522,65.0415,... 1.41478,2.52135,1.09140,... [M+H]+
#> 4 41.0424,56.0532,65.0403,... 6.06061,7.02479,4.68320,... [M+H]+
#> 5 42.0032,42.0105,67.0334,... 5.66221,3.25771,1.37677,... [M-H]-
#> ... ... ... ...
#> 26 266.248,311.306,494.457,... 60.0601,40.0400,30.0300,... [M+H]+
#> 27 266.248,311.306,494.457,... 60.0601,40.0400,30.0300,... [M+H]+
#> 28 266.248,311.306,494.457,... 60.0601,40.0400,30.0300,... [M+H]+
#> 29 266.248,311.306,494.457,... 60.0601,40.0400,30.0300,... [M+H]+
#> 30 266.248,311.306,494.457,... 60.0601,40.0400,30.0300,... [M+H]+
#> PrecursorMZ Collision_energy Ion_mode Spectrum_type
#> <character> <character> <character> <character>
#> 1 NA NA NA NA
#> 2 189.1603 NA NA NA
#> 3 265.1188 35 eV NA NA
#> 4 265.1188 45 eV NA NA
#> 5 263.1031 -35 eV NA NA
#> ... ... ... ... ...
#> 26 539.51462 NA P NA
#> 27 539.51462 NA P NA
#> 28 539.51462 NA P NA
#> 29 539.51462 NA P NA
#> 30 539.51462 NA P NA
#> dataOrigin msLevel
#> <character> <integer>
#> 1 /__w/_temp/Library/M.. 2
#> 2 /__w/_temp/Library/M.. 2
#> 3 /__w/_temp/Library/M.. 2
#> 4 /__w/_temp/Library/M.. 2
#> 5 /__w/_temp/Library/M.. 2
#> ... ... ...
#> 26 /__w/_temp/Library/M.. 2
#> 27 /__w/_temp/Library/M.. 2
#> 28 /__w/_temp/Library/M.. 2
#> 29 /__w/_temp/Library/M.. 2
#> 30 /__w/_temp/Library/M.. 2