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msTab-M ms_run metadata fields

Source: R/MTD.R
mtd_ms_run.Rd

The mtd_ms_run() function allows to define and format the ms_run fields of the mzTab-M metadata. The information is build on the actual data file names along with optional additional parameters to characterize the MS run(s).

For details and expected input for the various parameter it is strongly suggested to consult the mzTab-M documentation.

Usage

mtd_ms_run(
  location = character(),
  instrument_ref = integer(),
  format = character(),
  id_format = character(),
  fragmentation_method = vector("list", length(location)),
  scan_polarity = character(),
  hash = character(),
  hash_method = character()
)

Arguments

location

character with the location (and file name) of the individual runs. Each element will be one run. This parameter is required, set to "null" if the location of the file(s) is not known.

instrument_ref

(optional) integer() with the index of the instrument the run was measured on.

format

(optional) character defining the format of the external MS data file. If specified, also id_format has be be provided. Can be of length 1 or equal to length(location). For data file(s) in mzML format, format = "[MS, MS:1000584, mzML file, ]" can be used.

id_format

(optional) character defining the id format used in the external data file. If specified, also format needs to be defined. Can be of length 1 or equal to length(location). For data file(s) in mzML format, format = "[MS, MS:1000530, mzML unique identifier, ]" can be used.

fragmentation_method

(optional) list of character defining the type(s) of fragmentation(s) used in a given ms run. Length must match length of location if provided. If no fragmentation was used for a specific file/run use NULL for that list element (position). As example, if two runs are included, the first does not have any fragmentation and for the second CID and HCD was used define list(NULL, c("[MS, MS:1000133, CID, ]", "[MS, MS:1000422, HCD, ]")).

scan_polarity

character defining the polarity of a run. Can be either "positive" or "negative". Can be of length 1 or equal to length(location).

hash

(optional) character with the hash value of the corresponding external MS data file. If provided, also hash_method needs to be defined. The length of hash has to match the length of location.

hash_method

(optional) character with the hash method used to generate the value in hash. If provided, also hash needs to be defined. The length of hash_method has to match the length of hash.

Value

two column character matrix with the ms_run metadata fields for a mzTab-M file.

Note

At present only a single polarity per run/file is supported.

See also

MTD-export for other functions defining metadata information

Author

Johannes Rainer, Philippine Louail

Examples


## Build a very basic MTD ms_run section for two data files
fls <- c("file:///path/to/file/a.mzML", "file:///path/to/file/b.mzML")
mtd_ms_run(location = fls, scan_polarity = "positive")
#>                                   values                             
#> [1,] "ms_run[1]-location"         "file:///path/to/file/a.mzML"      
#> [2,] "ms_run[1]-scan_polarity[1]" "[MS, MS:1000130, positive scan, ]"
#> [3,] "ms_run[2]-location"         "file:///path/to/file/b.mzML"      
#> [4,] "ms_run[2]-scan_polarity[1]" "[MS, MS:1000130, positive scan, ]"

## Add also instrument reference information
mtd_ms_run(location = fls, scan_polarity = "positive", instrument_ref = 1)
#>                                   values                             
#> [1,] "ms_run[1]-location"         "file:///path/to/file/a.mzML"      
#> [2,] "ms_run[1]-instrument_ref"   "instrument[1]"                    
#> [3,] "ms_run[1]-scan_polarity[1]" "[MS, MS:1000130, positive scan, ]"
#> [4,] "ms_run[2]-location"         "file:///path/to/file/b.mzML"      
#> [5,] "ms_run[2]-instrument_ref"   "instrument[1]"                    
#> [6,] "ms_run[2]-scan_polarity[1]" "[MS, MS:1000130, positive scan, ]"

## Finally, add a fragmentation method used for the second file - no
## fragmentation was used for the first file, thus `NULL` is specified.
## Parameter `fragmentation_method` expects a `list` as input to support
## also multiple fragmentation methods per MS run.
mtd_ms_run(location = fls, scan_polarity = "positive",
    fragmentation_method = list(NULL, "[MS, MS:1000133, CID, ]"))
#>                                          values                             
#> [1,] "ms_run[1]-location"                "file:///path/to/file/a.mzML"      
#> [2,] "ms_run[1]-scan_polarity[1]"        "[MS, MS:1000130, positive scan, ]"
#> [3,] "ms_run[2]-location"                "file:///path/to/file/b.mzML"      
#> [4,] "ms_run[2]-fragmentation_method[1]" "[MS, MS:1000133, CID, ]"          
#> [5,] "ms_run[2]-scan_polarity[1]"        "[MS, MS:1000130, positive scan, ]"