ZenoTOF not in CV: Invalid cvParam accession "1003293"

[sneumann]

Hi, @RemyDeB reported sneumann/xcms#670
and indeed the ZenoTOF is in
https://github.com/HUPO-PSI/psi-ms-CV/blob/72ed99cae68f900a11cefb0d4aa7c39136484df3/psi-ms.obo#L21686
but not in the cv.* files in https://github.com/sneumann/mzR/tree/master/src/pwiz/data/common
This needs new files, possibly copied over from
https://github.com/ProteoWizard/pwiz/tree/master/pwiz/data/common
which is known to have the 1003293
https://github.com/ProteoWizard/pwiz/blob/f7165e119169b38ac3af6f5d29276f88ee1e30a9/pwiz/data/common/psi-ms.obo#L21686
Yours, Steffen

[RemyDeB]

Hi,
Do i have to create a pull request with right cv.* files analogous to #210 ?

Regards, Remy

[sneumann]

Hi, theoretically that would be great, but I was faster this time :-)
#279
BUT with that I get errors on R CMD check mzR because of:

Error: processing vignette 'mzR.Rmd' failed with diagnostics:
Can not open file /usr/local/lib/R/site-library/msdata/threonine/threonine_i2_e35_pH_tree.mzXML! 
Original error was: 
Error in eval(expr, envir, enclos): 
[CVTranslator::insert()] Collision: 1001339 1002707

I don't yet know what that means (I guess either the CV maintainers or some converters messed up somewhere, and now pwiz finds and barfs on that). I don't know if I need to fix the ancient test file in msdata package, or something in the code.
Good news: you can install the branch https://github.com/sneumann/mzR/tree/fix/issue278 locally and fix your problem.
Yours,
Steffen

[sneumann]

These indeed have a very similar name:

[Term]
id: MS:1001339
name: (?<=[KR])
def: "Regular expression for Trypsin/P." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

and

[Term]
id: MS:1002707
name: (?=[KR])
def: "Regular expression for LysargiNase." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

[RemyDeB]

Hi, Can install the branch locally but got the same error as yours when i run readMSData.

traceback :
7: stop(structure(list(message = "[CVTranslator::insert()] Collision: 1001339 1002707", call = NULL, cppstack = NULL), class = c("std::runtime_error", "C++Error", "error", "condition"))) 6: .External(structure(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x0000021596693c10>, dll = structure(list( name = "Rcpp", path = "C:/Users/remyd/AppData/Local/R/win-library/4.2/Rcpp/libs/x64/Rcpp.dll", dynamicLookup = TRUE, handle = <pointer: 0x00007fff882a0000>, info = <pointer: 0x0000021597699d00>), class = "DLLInfo"), numParameters = -1L), class = c("ExternalRoutine", "NativeSymbolInfo" )), <pointer: 0x000002159b87c700>, <pointer: 0x0000021597fe3fc0>, .pointer) 5: object@backend$getInstrumentInfo() 4: instrumentInfo(msdata) 3: instrumentInfo(msdata) 2: readOnDiskMSData(files = files, pdata = pdata, msLevel. = msLevel., verbose = verbose, centroided. = centroided., smoothed. = smoothed.) 1: readMSData(dda_file, mode = "onDisk")

Your guess seems to be right, looks like a typing error
I don't know if it's usefull to keep cleavage agents in our case maybe can delete this lines and wait for a patch ?

Regards, Remy

[sneumann]

Nope, I am not gonna touch (and maintain those changes throughout updates ...) the psi-ms.obo file.
Instead, I pulled in newer CVTranslator files which seem to circumvent the issue https://github.com/sneumann/mzR/commits/fix/issue278
So for me R CMD check now passes, and if you confirm I can merge.
Yours, Steffen

[RemyDeB]

New version works well can read .mzXL files of ZenoTOF.

Yours , Remy