There are also a lot of useful tools in metid.

library(metid)
#> metid 1.2.24 (2022-09-19 17:11:25)
#> 
#> Attaching package: 'metid'
#> The following object is masked from 'package:stats':
#> 
#>     filter
library(tidyverse)
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
#>  tibble  3.1.7           purrr   0.3.4     
#>  tidyr   1.2.0           stringr 1.4.1     
#>  readr   2.1.2           forcats 0.5.1.9000
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#>  MSnbase::combine()       masks Biobase::combine(), BiocGenerics::combine(), dplyr::combine()
#>  tidyr::expand()          masks S4Vectors::expand()
#>  tidyr::extract()         masks magrittr::extract()
#>  massdataset::filter()    masks dplyr::filter(), metid::filter(), stats::filter()
#>  S4Vectors::first()       masks dplyr::first()
#>  dplyr::lag()             masks stats::lag()
#>  BiocGenerics::Position() masks ggplot2::Position(), base::Position()
#>  purrr::reduce()          masks MSnbase::reduce()
#>  S4Vectors::rename()      masks massdataset::rename(), dplyr::rename()
#>  purrr::set_names()       masks magrittr::set_names()

Read MS2 data

Read msp format file using readMGF

result <- readMGF(file)

Read mzXML format file using readMZXML

result <- readMZXML(file, threads = 3)

Read MGF format file using readMGF

result <- readMGF(file)
metid::metid_logo()
#> Thank you for using metid!
#> Version 1.2.24 (2022-09-19 17:11:25)
#> More information: metid.tidymass.org
#>                 _    _____  ___ 
#>  _ __ ___   ___| |_  \_   \/   \
#> | '_ ` _ \ / _ \ __|  / /\/ /\ /
#> | | | | | |  __/ |_/\/ /_/ /_// 
#> |_| |_| |_|\___|\__\____/___,'  
#> 

Session information

sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] tinytools_0.9.1    forcats_0.5.1.9000 stringr_1.4.0      dplyr_1.0.9       
#>  [5] purrr_0.3.4        readr_2.1.2        tidyr_1.2.0        tibble_3.1.7      
#>  [9] tidyverse_1.3.1    ggplot2_3.3.6      massdataset_1.0.5  magrittr_2.0.3    
#> [13] masstools_0.99.13  metid_1.2.17      
#> 
#> loaded via a namespace (and not attached):
#>   [1] backports_1.4.1             readxl_1.4.0               
#>   [3] circlize_0.4.15             systemfonts_1.0.4          
#>   [5] plyr_1.8.7                  lazyeval_0.2.2             
#>   [7] BiocParallel_1.30.3         listenv_0.8.0              
#>   [9] GenomeInfoDb_1.32.2         Rdisop_1.56.0              
#>  [11] digest_0.6.29               foreach_1.5.2              
#>  [13] yulab.utils_0.0.5           htmltools_0.5.2            
#>  [15] fansi_1.0.3                 memoise_2.0.1              
#>  [17] cluster_2.1.3               doParallel_1.0.17          
#>  [19] tzdb_0.3.0                  openxlsx_4.2.5             
#>  [21] limma_3.52.2                ComplexHeatmap_2.12.0      
#>  [23] globals_0.15.1              modelr_0.1.8               
#>  [25] matrixStats_0.62.0          pkgdown_2.0.5              
#>  [27] prettyunits_1.1.1           colorspace_2.0-3           
#>  [29] rvest_1.0.2                 haven_2.5.0                
#>  [31] textshaping_0.3.6           xfun_0.31                  
#>  [33] crayon_1.5.1                RCurl_1.98-1.7             
#>  [35] jsonlite_1.8.0              impute_1.70.0              
#>  [37] iterators_1.0.14            glue_1.6.2                 
#>  [39] gtable_0.3.0                zlibbioc_1.42.0            
#>  [41] XVector_0.36.0              GetoptLong_1.0.5           
#>  [43] DelayedArray_0.22.0         shape_1.4.6                
#>  [45] BiocGenerics_0.42.0         scales_1.2.0               
#>  [47] vsn_3.64.0                  DBI_1.1.3                  
#>  [49] Rcpp_1.0.8.3                mzR_2.30.0                 
#>  [51] viridisLite_0.4.0           progress_1.2.2             
#>  [53] clue_0.3-61                 gridGraphics_0.5-1         
#>  [55] preprocessCore_1.58.0       stats4_4.2.1               
#>  [57] MsCoreUtils_1.8.0           htmlwidgets_1.5.4          
#>  [59] httr_1.4.3                  RColorBrewer_1.1-3         
#>  [61] ellipsis_0.3.2              pkgconfig_2.0.3            
#>  [63] XML_3.99-0.10               dbplyr_2.2.1               
#>  [65] sass_0.4.1                  utf8_1.2.2                 
#>  [67] ggplotify_0.1.0             tidyselect_1.1.2           
#>  [69] rlang_1.0.3                 munsell_0.5.0              
#>  [71] cellranger_1.1.0            tools_4.2.1                
#>  [73] cachem_1.0.6                cli_3.3.0                  
#>  [75] generics_0.1.3              broom_1.0.0                
#>  [77] evaluate_0.15               fastmap_1.1.0              
#>  [79] mzID_1.34.0                 yaml_2.3.5                 
#>  [81] ragg_1.2.2                  knitr_1.39                 
#>  [83] fs_1.5.2                    zip_2.2.0                  
#>  [85] ncdf4_1.19                  pbapply_1.5-0              
#>  [87] future_1.26.1               xml2_1.3.3                 
#>  [89] compiler_4.2.1              rstudioapi_0.13            
#>  [91] plotly_4.10.0               png_0.1-7                  
#>  [93] affyio_1.66.0               reprex_2.0.1               
#>  [95] bslib_0.3.1                 stringi_1.7.6              
#>  [97] desc_1.4.1                  MSnbase_2.22.0             
#>  [99] lattice_0.20-45             ProtGenerics_1.28.0        
#> [101] Matrix_1.4-1                ggsci_2.9                  
#> [103] vctrs_0.4.1                 pillar_1.7.0               
#> [105] lifecycle_1.0.1             furrr_0.3.0                
#> [107] BiocManager_1.30.18         jquerylib_0.1.4            
#> [109] MALDIquant_1.21             GlobalOptions_0.1.2        
#> [111] data.table_1.14.2           bitops_1.0-7               
#> [113] GenomicRanges_1.48.0        R6_2.5.1                   
#> [115] pcaMethods_1.88.0           affy_1.74.0                
#> [117] IRanges_2.30.0              parallelly_1.32.0          
#> [119] codetools_0.2-18            MASS_7.3-57                
#> [121] assertthat_0.2.1            SummarizedExperiment_1.26.1
#> [123] rprojroot_2.0.3             rjson_0.2.21               
#> [125] withr_2.5.0                 S4Vectors_0.34.0           
#> [127] GenomeInfoDbData_1.2.8      parallel_4.2.1             
#> [129] hms_1.1.1                   grid_4.2.1                 
#> [131] rmarkdown_2.14              MatrixGenerics_1.8.1       
#> [133] lubridate_1.8.0             Biobase_2.56.0