Error for XIC plot of timsTof data

[NorStorz]

Hi, i run into the following error when i try to call plot(mse, type = "XIC") on timfTOF data with MsBackendTimsTof:

Error in rep(rtime(z), lns) : invalid 'times' argument

This example should be reproducible:

library(xcms)
library(MsExperiment)
library(opentimsr)
library(MsBackendTimsTof)

so_folder <- tempdir()
so_file <- download_bruker_proprietary_code(so_folder, method = "wget")
setup_bruker_so(so_file)

link <- "[https://www.biosino.org/download/node/data/public/OED788908"](https://www.biosino.org/download/node/data/public/OED788908%22)
download.file(link ,destfile="dat.tar.gz")
untar("dat.tar.gz")

fls <- "12_serial_diluted_urine_neg/1X/04_1X_nist_urine_neg_6_p1-a1_1_7154.d"

mse <- readMsExperiment(fls, source = MsBackendTimsTof())

plot(mse, type = "XIC")

From the traceback i could find out that the error occurs inside the function .xmse_plot_xic I tested it with the following code:

msLevel = 1L
z <- mse[1]
lst <- as(filterMsLevel(spectra(z), msLevel = msLevel), "list")
lns <- lengths(lst) / 2
lst <- do.call(rbind, lst)
df <- data.frame(rt = rep(rtime(z), lns), lst)

The problem seems to be that rtime(z) and 'lns' differ in length. This is probably caused by the MS1 filtering of the Spectra:

> length(rtime(z))
[1] 1839591
> length(spectra(z))
[1] 1839591
> length(lns)
[1] 1260153
> length(as(filterMsLevel(spectra(z), msLevel = 1L), "list"))
[1] 1260153

This is my session info:

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
[9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] devtools_2.4.5         usethis_2.2.2          viridis_0.6.5         
[4] viridisLite_0.4.2      opentimsr_1.0.13       MsExperiment_1.4.0    
[7] xcms_4.0.2             MSnbase_2.28.1         mzR_2.36.0            
[10] Rcpp_1.0.12            Biobase_2.62.0         MsBackendTimsTof_0.1.5
[13] Spectra_1.12.0         ProtGenerics_1.34.0    BiocParallel_1.36.0   
[16] S4Vectors_0.40.2       BiocGenerics_0.48.1   
...

[jorainer]

Hm, strange error. Can you please run table(msLevel(mse)) - I would assume you have MS1 and MS2 spectra in your data set?

If we call rtime on the full object (MsExperiment/XcmsExperiment) and as(..., "list") only on the data set filtered for one MS level than we have indeed a bug... PR with a fix would be highly welcome :)

Also, have you tried to run plot without type = "XIC"? I think, for MsExperiment the plot is always the type XIC.

[NorStorz]

Hi, Yes i have MS1 and MS2 spectra in my data set. table(msLevel(spectra(mse))) returns:

      1       2 
1260153  579438  

And plot(mse) also leads to the error. And it seems to be a problem for all LC-MS/MS data. I tried some data from the msdata package, which also caused the error:

library("msdata")
FilePaths <- msdata::proteomics(full.names=TRUE)
mse_test <- readMsExperiment(FilePaths[4])
plot(mse_test)

I will look into this and create a PR.

[jorainer]

Great! Thanks @NorStorz - let me know if you need some help or if something is unclear.