I am trying to add mzIdent data to an MSnExp (which comes from an mgf file). addIdentificationData gives me an error:

Error in strsplit(ssv, sep) : non-character argument

The same error is produced if I provide z='path/to/mzID file' or read in the file with mzID('path/to/mzID file') first and just use the mzID object. I saw this was reported before, but I am using the latest version that should not have this problem.

Thank you for your help, Janos

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] mzID_1.22.0           RforProteomics_1.22.0 MSnbase_2.10.1        ProtGenerics_1.16.0   S4Vectors_0.22.0      mzR_2.18.0            Rcpp_1.0.1           
 [8] Biobase_2.44.0        BiocGenerics_0.30.0   forcats_0.4.0         stringr_1.4.0         purrr_0.3.2           readr_1.3.1           tidyr_0.8.3          
[15] tibble_2.1.3          ggplot2_3.2.0         tidyverse_1.2.1       dplyr_0.8.1           data.table_1.12.2    

loaded via a namespace (and not attached):
 [1] nlme_3.1-140          bitops_1.0-6          lubridate_1.7.4       doParallel_1.0.14     httr_1.4.0            tools_3.6.0           backports_1.1.4      
 [8] R6_2.4.0              affyio_1.54.0         lazyeval_0.2.2        colorspace_1.4-1      withr_2.1.2           tidyselect_0.2.5      compiler_3.6.0       
[15] preprocessCore_1.46.0 graph_1.62.0          cli_1.1.0             rvest_0.3.4           xml2_1.2.0            labeling_0.3          scales_1.0.0         
[22] affy_1.62.0           RBGL_1.60.0           digest_0.6.19         R.utils_2.9.0         pkgconfig_2.0.2       htmltools_0.3.6       limma_3.40.2         
[29] rlang_0.3.4           readxl_1.3.1          rstudioapi_0.10       impute_1.58.0         shiny_1.3.2           generics_0.0.2        jsonlite_1.6         
[36] BiocParallel_1.18.0   R.oo_1.22.0           RCurl_1.95-4.12       magrittr_1.5          MALDIquant_1.19.3     munsell_0.5.0         R.methodsS3_1.7.1    
[43] vsn_3.52.0            stringi_1.4.3         MASS_7.3-51.4         zlibbioc_1.30.0       biocViews_1.52.2      plyr_1.8.4            grid_3.6.0           
[50] promises_1.0.1        crayon_1.3.4          lattice_0.20-38       haven_2.1.0           hms_0.4.2             pillar_1.4.1          RUnit_0.4.32         
[57] codetools_0.2-16      XML_3.98-1.20         glue_1.3.1            pcaMethods_1.76.0     BiocManager_1.30.4    modelr_0.1.4          httpuv_1.5.1         
[64] foreach_1.4.4         cellranger_1.1.0      gtable_0.3.0          assertthat_0.2.1      mime_0.7              xtable_1.8-4          broom_0.5.2          
[71] later_0.8.0           ncdf4_1.16.1          iterators_1.0.10      IRanges_2.18.1  

The previous post to refer to is different than you issue. In your case, unfortunately, the addIdentificationData will not work as it expects to find information that it can't find when reading data from an mgf file. This code was written for the more complete mzML format in mind.

What you can however do it to read the identification data in as a data.frame with readMzIdData, filter it with filterIdentificationDataFrame (as is done in addIdentificationData). This should give you a spectrum.title column in the identification data.frame, that you will be able to match to the TITLE feature variable (fData) of your raw data object.