msms_spectra_hmdb imports MS/MS spectra from corresponding xml files from
HMDB (http://www.hmdb.ca) and returns the data as a data.frame. HMDB
stores MS/MS spectrum data in xml files, one file per spectrum.
Depending on the parameter collapsed, the returned data.frame is either
collapsed, meaning that each row represents data from one spectrum xml
file, or expanded with one row for each m/z and intensity pair for each
spectrum. Columns "mz" and "intensity" are of type list for
collapsed = TRUE and numeric for collapsed = FALSE.
Arguments
- x
character(1): with the path to directory containing the xml files.- collapsed
logical(1)whether the returneddata.frameshould be collapsed or expanded. See description for more details.
Value
data.frame with as many rows as there are peaks and columns:
spectrum_id (
integer): an arbitrary, unique ID identifying values from one xml file.original_spectrum_id (
character): the HMDB-internal ID of the spectrum.compound_id (
character): the HMDB compound ID the spectrum is associated with.polarity (
integer): 0 for negative, 1 for positive,NAfor not set.collision_energy (
numeric): collision energy voltage.predicted (
logical): whether the spectrum is predicted or experimentally verified.splash (
character): the SPLASH (SPectraL hASH) key of the spectrum (Wohlgemuth 2016).instrument_type (
character): the type of MS instrument on which the spectrum was measured.instrument (
character): the MS instrument (not available for all spectra in HMDB).precursor_mz (
numeric): not provided by HMDB and thusNA.mz (
numericorlistofnumeric): m/z values of the spectrum.intensity (
numericorlistofnumeric): intensity of the spectrum.
Note
The HMDB xml files are supposed to be extracted from the downloaded zip file into a folder and should not be renamed. The function identifies xml files containing MS/MS spectra by their file name.
The same spectrum ID can be associated with multiple compounds. Thus, the
function assignes an arbitrary ID (column "spectrum_id") to values from
each file. The original ID of the spectrum in HMDB is provided in column
"original_spectrum_id".
References
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Selak RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. SPLASH, A hashed identifier for mass spectra. Nature Biotechnology 2016 34(11):1099-1101
See also
createCompDb() for the function to create a CompDb database with
compound annotation and spectrum data.
Other spectrum data import functions.:
msms_spectra_mona()
Examples
## Locate the folder within the package containing test xml files.
pth <- system.file("xml", package = "CompoundDb")
## List all files in that directory
dir(pth)
#> [1] "HMDB0000001_ms_ms_spectrum_1_experimental.xml"
#> [2] "HMDB0000001_ms_ms_spectrum_2_experimental.xml"
#> [3] "HMDB0004370_ms_ms_spectrum_446575_experimental.xml"
#> [4] "HMDB0006719_ms_ms_spectrum_370739_predicted.xml"
#> [5] "fail"
## Import spectrum data from HMDB MS/MS spectrum xml files in that directory
msms_spectra_hmdb(pth)
#> Going to process 4 xml files.
#> Postprocessing data ...
#> OK
#> original_spectrum_id compound_id polarity collision_energy predicted
#> 1 1 HMDB0000001 1 10 FALSE
#> 2 2 HMDB0000001 1 25 FALSE
#> 3 446575 HMDB0004370 1 NA FALSE
#> 4 370739 HMDB0006719 0 20 TRUE
#> splash instrument_type
#> 1 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 2 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 3 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 4 splash10-001i-0009000000-c16445787a057993951a <NA>
#> instrument precursor_mz mz intensity
#> 1 <NA> NA 109.2, 1.... 3.406999....
#> 2 <NA> NA 83.1, 96.... 6.685028....
#> 3 API3000, Applied Biosystems NA 44.1, 57.... 0.051124....
#> 4 <NA> NA 111.0815.... 0.550973....
#> spectrum_id
#> 1 1
#> 2 2
#> 3 3
#> 4 4
## Import the data as an *expanded* data frame, i.e. with a row for each
## single m/z (intensity) value.
msms_spectra_hmdb(pth, collapsed = FALSE)
#> Going to process 4 xml files.
#> Postprocessing data ...
#> OK
#> original_spectrum_id compound_id polarity collision_energy predicted
#> 1 1 HMDB0000001 1 10 FALSE
#> 2 1 HMDB0000001 1 10 FALSE
#> 3 1 HMDB0000001 1 10 FALSE
#> 4 1 HMDB0000001 1 10 FALSE
#> 5 1 HMDB0000001 1 10 FALSE
#> 6 2 HMDB0000001 1 25 FALSE
#> 7 2 HMDB0000001 1 25 FALSE
#> 8 2 HMDB0000001 1 25 FALSE
#> 9 2 HMDB0000001 1 25 FALSE
#> 10 2 HMDB0000001 1 25 FALSE
#> 11 2 HMDB0000001 1 25 FALSE
#> 12 2 HMDB0000001 1 25 FALSE
#> 13 446575 HMDB0004370 1 NA FALSE
#> 14 446575 HMDB0004370 1 NA FALSE
#> 15 446575 HMDB0004370 1 NA FALSE
#> 16 446575 HMDB0004370 1 NA FALSE
#> 17 446575 HMDB0004370 1 NA FALSE
#> 18 446575 HMDB0004370 1 NA FALSE
#> 19 446575 HMDB0004370 1 NA FALSE
#> 20 446575 HMDB0004370 1 NA FALSE
#> 21 446575 HMDB0004370 1 NA FALSE
#> 22 446575 HMDB0004370 1 NA FALSE
#> 23 446575 HMDB0004370 1 NA FALSE
#> 24 446575 HMDB0004370 1 NA FALSE
#> 25 446575 HMDB0004370 1 NA FALSE
#> 26 446575 HMDB0004370 1 NA FALSE
#> 27 446575 HMDB0004370 1 NA FALSE
#> 28 446575 HMDB0004370 1 NA FALSE
#> 29 446575 HMDB0004370 1 NA FALSE
#> 30 446575 HMDB0004370 1 NA FALSE
#> 31 446575 HMDB0004370 1 NA FALSE
#> 32 446575 HMDB0004370 1 NA FALSE
#> 33 446575 HMDB0004370 1 NA FALSE
#> 34 446575 HMDB0004370 1 NA FALSE
#> 35 446575 HMDB0004370 1 NA FALSE
#> 36 446575 HMDB0004370 1 NA FALSE
#> 37 446575 HMDB0004370 1 NA FALSE
#> 38 446575 HMDB0004370 1 NA FALSE
#> 39 446575 HMDB0004370 1 NA FALSE
#> 40 446575 HMDB0004370 1 NA FALSE
#> 41 446575 HMDB0004370 1 NA FALSE
#> 42 446575 HMDB0004370 1 NA FALSE
#> 43 446575 HMDB0004370 1 NA FALSE
#> 44 446575 HMDB0004370 1 NA FALSE
#> 45 446575 HMDB0004370 1 NA FALSE
#> 46 370739 HMDB0006719 0 20 TRUE
#> 47 370739 HMDB0006719 0 20 TRUE
#> 48 370739 HMDB0006719 0 20 TRUE
#> 49 370739 HMDB0006719 0 20 TRUE
#> 50 370739 HMDB0006719 0 20 TRUE
#> 51 370739 HMDB0006719 0 20 TRUE
#> 52 370739 HMDB0006719 0 20 TRUE
#> 53 370739 HMDB0006719 0 20 TRUE
#> 54 370739 HMDB0006719 0 20 TRUE
#> 55 370739 HMDB0006719 0 20 TRUE
#> splash instrument_type
#> 1 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 2 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 3 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 4 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 5 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 6 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 7 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 8 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 9 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 10 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 11 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 12 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 13 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 14 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 15 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 16 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 17 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 18 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 19 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 20 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 21 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 22 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 23 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 24 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 25 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 26 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 27 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 28 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 29 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 30 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 31 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 32 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 33 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 34 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 35 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 36 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 37 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 38 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 39 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 40 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 41 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 42 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 43 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 44 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 45 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 46 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 47 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 48 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 49 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 50 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 51 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 52 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 53 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 54 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 55 splash10-001i-0009000000-c16445787a057993951a <NA>
#> instrument precursor_mz mz intensity spectrum_id
#> 1 <NA> NA 109.2000 3.4069998 1
#> 2 <NA> NA 124.2000 47.4945731 1
#> 3 <NA> NA 124.5000 3.0943658 1
#> 4 <NA> NA 170.1600 100.0000000 1
#> 5 <NA> NA 170.5200 13.2396932 1
#> 6 <NA> NA 83.1000 6.6850283 2
#> 7 <NA> NA 96.1200 4.3812987 2
#> 8 <NA> NA 97.1400 3.0221439 2
#> 9 <NA> NA 109.1400 16.7082568 2
#> 10 <NA> NA 124.0800 100.0000000 2
#> 11 <NA> NA 125.1000 4.5651409 2
#> 12 <NA> NA 170.1600 40.6434125 2
#> 13 API3000, Applied Biosystems NA 44.1000 0.0511240 3
#> 14 API3000, Applied Biosystems NA 57.9000 0.0065970 3
#> 15 API3000, Applied Biosystems NA 61.4000 0.0120940 3
#> 16 API3000, Applied Biosystems NA 71.2000 0.0016490 3
#> 17 API3000, Applied Biosystems NA 73.8000 0.0032980 3
#> 18 API3000, Applied Biosystems NA 78.3000 0.0060470 3
#> 19 API3000, Applied Biosystems NA 78.8000 0.0049480 3
#> 20 API3000, Applied Biosystems NA 83.1000 0.0153920 3
#> 21 API3000, Applied Biosystems NA 88.2000 0.0038480 3
#> 22 API3000, Applied Biosystems NA 98.8000 0.0087960 3
#> 23 API3000, Applied Biosystems NA 101.7000 0.0038480 3
#> 24 API3000, Applied Biosystems NA 102.8000 0.0021990 3
#> 25 API3000, Applied Biosystems NA 106.8000 0.0109940 3
#> 26 API3000, Applied Biosystems NA 111.6000 0.0038480 3
#> 27 API3000, Applied Biosystems NA 115.1000 0.1016990 3
#> 28 API3000, Applied Biosystems NA 116.9000 0.0555220 3
#> 29 API3000, Applied Biosystems NA 118.1000 0.4254850 3
#> 30 API3000, Applied Biosystems NA 121.0000 0.0082460 3
#> 31 API3000, Applied Biosystems NA 124.9000 0.0087960 3
#> 32 API3000, Applied Biosystems NA 126.7000 0.0032980 3
#> 33 API3000, Applied Biosystems NA 127.2000 0.0115440 3
#> 34 API3000, Applied Biosystems NA 128.9000 0.0038480 3
#> 35 API3000, Applied Biosystems NA 129.9000 0.0164920 3
#> 36 API3000, Applied Biosystems NA 131.9000 8.9527790 3
#> 37 API3000, Applied Biosystems NA 139.0000 0.0241880 3
#> 38 API3000, Applied Biosystems NA 140.4000 0.0115440 3
#> 39 API3000, Applied Biosystems NA 141.2000 0.0588200 3
#> 40 API3000, Applied Biosystems NA 142.9000 0.0571710 3
#> 41 API3000, Applied Biosystems NA 144.1000 36.3817270 3
#> 42 API3000, Applied Biosystems NA 157.6000 0.0357320 3
#> 43 API3000, Applied Biosystems NA 158.0000 0.3848060 3
#> 44 API3000, Applied Biosystems NA 175.2000 100.0000000 3
#> 45 API3000, Applied Biosystems NA 193.2000 0.0087960 3
#> 46 <NA> NA 111.0815 0.5509733 4
#> 47 <NA> NA 249.2588 0.7330056 4
#> 48 <NA> NA 273.2588 0.5171464 4
#> 49 <NA> NA 341.2850 0.6527944 4
#> 50 <NA> NA 353.3214 0.8764642 4
#> 51 <NA> NA 355.3006 0.7582467 4
#> 52 <NA> NA 355.3370 0.4985064 4
#> 53 <NA> NA 365.3214 21.2824831 4
#> 54 <NA> NA 367.3006 2.4354476 4
#> 55 <NA> NA 383.3319 52.1357554 4