jorainer
export massbank spectra object 2 mgf format encounter error.
Sorry for bombarding questions here! This question is not urgent but I would like to see if you can tell what is going wrong.
When I try to export massbank spectra object to mgf file, I encounter this error:
Error in .export_mgf(x = x, con = file, mapping = mapping) :
Column(s) synonym contain multiple elements per row. Please either drop this column or reduce its elements to a single value per row.
I do find out that some of the SpectraVaribles may indeed have multiple elements per row?
Below I extract one massbank spectra object by calling spectraData() and then manually transformed it vertically.
msLevel 2
rtime NA
acquisitionNum NA
scanIndex NA
dataStorage <MassBank>
dataOrigin NA
centroided NA
smoothed NA
polarity 0
precScanNum NA
precursorMz 506
precursorIntensity 408.000305
precursorCharge NA
collisionEnergy NA
isolationWindowLowerMz NA
isolationWindowTargetMz NA
isolationWindowUpperMz NA
spectrum_id MCH00020
spectrum_name Adenosine 5'-triphosphate; LC-ESI-ITFT; MS2; [M-H]-
date 2016.01.19 (Created 2011.01.06, modified 2011.08.03)
authors Yoshikuni K, Tajiri M, Wada Y, Osaka Medical Center for Maternal and Child Health
license CC BY-SA
copyright NA
publication NA
splash splash10-0a4i-0000900000-e9a09b9360491c310280
compound_id 1
adduct [M-H]-
ionization NA
ionization_voltage NA
fragmentation_mode NA
collision_energy_text NA
instrument LTQ Orbitrap XL, Thermo Scientific
instrument_type LC-ESI-ITFT
formula C10H16N5O13P3
exactmass 506.99575
smiles Nc(n3)c(n2)c(nc3)n(c2)[C@]([H])(O1)[C@]([H])(O)[C@]([H])(O)[C@@]([H])(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)1
inchi InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
inchikey ZKHQWZAMYRWXGA-KQYNXXCUSA-N
cas 56-65-5
pubchem CID:5957
synonym c("Adenosine 5'-triphosphate"
precursor_mz_text "ATP")
compound_name 506
Adenosine 5'-triphosphate
However, I do not know how to fix this. Could you shoot me anything that may help? Thanks very much!
Best, Minghao
And BTW, why the precursorMz is integer? 506? Should it keep at least four digits after?
precursorMz 506
precursor_mz_text 506
you would have to check if any of the spectraData variables is of type "list" or "List" and then either drop or collapse them. A possible solution could be:
.is_list <- function(x) {
is.list(x) || inherits(x, "List")
}
SD <- spectraData(sps)
idx <- which(vapply(SD, .is_list, logical(1)))
for (i in idx) {
SD[, i] <- vapply(SD[, i], paste, FUN.VALUE = character(1), collapse = ";")
}
spectraData(sps) <- SD
This code will replace all columns in the spectra data that are of type list or List into a character column with the elements per row being collapsed by ";", i.e. if before you had e.g. in a column "synonym" multiple values per row c("a", "b", "c"), these will be combined into a single value per row "a;b;c".
Regarding the precursorMz, it depends what the actual value is (i.e. what is reported in MassBank or your mzML files). What is the $precursorMz in the original spectra? is it already 506 there are is there another number?
