Generated mzMLs contain `value="nan"` instead of `value="NaN"`

[Adafede]

Hi @sneumann,

I am using the mzR backend to export centroided spectra in mzML (see https://github.com/Adafede/CentroidR).
Actually, it seems that mzR exports value="nan" instead of value="NaN", which then leads to errors when reading the files in external tools.

I hacked a dirty fix to replace them manually (Adafede/CentroidR@eb9f6b3#diff-b4b5123cd43ca39308335e7138ce84d953d541808b220d786e239d4b18e9e349R156-R162) but this should be ideally fixed upstream?

Best,

Adriano

[sneumann]

Interesting. Can one reproduce that with plain proteowizard ?
Can one "convert" an mzML file with NaN in them, and check whether the output contains nan ? And the other way around ?
I quickly checked the specification at https://www.psidev.info/mzml and did not find anything about NaN vs nan (vs. null).
There is some information in https://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html#encoding-missing-values-zeroes-nulls-infinity-and-calculation-errors
which references https://www.w3.org/TR/xmlschema-2/#decimal and NaN indeed seems the correct(er) choice.
Yours,
Steffen

[Adafede]

Here a small reprex:

library(mzR)
#> Loading required package: Rcpp
#> Warning in fun(libname, pkgname): mzR has been built against a different Rcpp version (1.0.14)
#> than is installed on your system (1.1.0). This might lead to errors
#> when loading mzR. If you encounter such issues, please send a report,
#> including the output of sessionInfo() to the Bioc support forum at 
#> https://support.bioconductor.org/. For details see also
#> https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
test_file <- system.file("microtofq", "MM14.mzML", package = "msdata")
test_output_normal <- "test_normal.mzML"
test_output_nan <- "test_nan.mzML"

in_file <- mzR::openMSfile(filename = test_file, backend = "pwiz")
hdr <- mzR::header(object = in_file)
pks <- mzR::peaks(object = in_file)
mzR::close(con = in_file)
mzR::copyWriteMSData(original_file = test_file, file = test_output_normal, header = hdr, object = pks)

hdr$collisionEnergy[1] <- 0
hdr$precursorMZ[1] <- 123.4567
hdr$precursorCharge[1] <- 1L
hdr$precursorIntensity[1] <- 0
hdr$isolationWindowTargetMZ[1] <- 123.4567
mzR::copyWriteMSData(original_file = test_file, file = test_output_nan, header = hdr, object = pks)


check_nan_in_file <- function(file_path) {
  found <- readLines(con = file_path, warn = FALSE) |>
    grepl(pattern = 'value="nan"', fixed = TRUE) |>
    any()

  if (found) {
    message("The file contains value=\"nan\"")
    return(TRUE)
  } else {
    message("The file does NOT contain value=\"nan\"")
    return(FALSE)
  }
}

check_nan_in_file(test_output_normal)
#> The file does NOT contain value="nan"
#> [1] FALSE
check_nan_in_file(test_output_nan)
#> The file contains value="nan"
#> [1] TRUE

^{Created on 2025-08-12 with reprex v2.1.1}