Question: Adding Identification Data to MSnbase MSn Experiment
gravatar for lau1
2.0 years ago by
lau10 wrote:

Has anyone tried loading an mzid file generated by Comet/PWIZ into MSnbase MSn Experiment data? I was able to read the mzid file with mzID but addIdentificationData() gave an error (Error in split.default(x, g) : first argument must be a vector).

So far I have only been able to read mzid files generated by MSGF+ - but MSGF+ is missing some features I need so I am hoping to load comet or tide results.







> test_mzid <- mzID::mzID("~/Hela_120min_500ng_retry.mzid")

> test_mzid@parameters
An mzIDparameters object:

Software used:   Comet (version: 2017.01 rev. 0)
                 ProteoWizard software (version 3.0.11392)

Rawfile:         /home/Boreas/data2/ms/201710_ms/Hela_120min_500ng_retry

Database:        /home/Zephyr/annotations/fasta/Swissprot/20160920_Sp_Hs_Canonical_20183e.fasta
> test_mzid@psm
An mzIDpsm object with 50973 scans and 254546 psm's
> test_mzid@peptides
An mzIDpeptides object containing: 231848 peptides (91171 modified)
> test_mzid@evidence
An mzIDevidence object with 279934 entries
> test_mzid@database
An mzIDdatabase object with 19773 entries

> ms
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 15.29 Mb
- - - Spectra data - - -
 MS level(s): 1 2 
 Number of spectra: 74090 
 MSn retention times: 0:0 - 120:0 minutes
- - - Processing information - - -
Data loaded [Tue Oct 10 18:47:25 2017] 
 MSnbase version: 2.2.0 
- - - Meta data  - - -
  rowNames: Hela_120min_500ng_retry.mzML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
protocolData: none
  featureNames: X00001.1 X00002.1 ... X74090.1 (74090 total)
  fvarLabels: fileIdx spIdx ... spectrum (27 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'

> ms <- addIdentificationData(ms, id = "~/Boreas/data2/ms/201710_ms/Hela_120min_500ng_retry.mzid", verbose=TRUE)
reading Hela_120min_500ng_retry.mzid... DONE!
Error in split.default(x, g) : first argument must be a vector

msnbase • 318 views
ADD COMMENTlink written 2.0 years ago by lau10

Could you provide your sessionInfo() output, please. It would probably also easier to help with the raw and corresponding mzid files?

ADD REPLYlink written 2.0 years ago by Laurent Gatto1.2k
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