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Question: Adding Identification Data to MSnbase MSn Experiment
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gravatar for lau1
5 weeks ago by
lau10
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.

Thanks,

Edward

 

 

 

 

> 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  - - -
phenoData
  rowNames: Hela_120min_500ng_retry.mzML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  Hela_120min_500ng_retry.mzML 
protocolData: none
featureData
  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

ADD COMMENTlink written 5 weeks 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 5 weeks ago by Laurent Gatto840
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