update pwiz to 3.0.22047

[hechth]

With the new release for the ThermoRawFileParser planned here, the current implementation of mzR won't be able to read the new mzml files due to the accession number.

Since ProteoWizard version 3.0.22047 seems to be handle those files, it would be great to update mzR before the new ThermoRawFileParser update.

[caetera]

A small clarification, according to this issue https://github.com/ProteoWizard/pwiz/issues/1540, the support for a new CV term for ThermoRawFileParser has been implemented in pwiz since around Aug 2021, i.e. all the releases from that on can be used as well (if somehow necessary). Please, let me know if you need a sample for testing

[jorainer]

Thanks @hechth for the heads-up - and @caetera , yes, indeed, would be nice to get a test file to see if mzR actually breaks and validate eventual fixes.

[caetera]

Hi @jorainer,

you can have a "sample" using that link: https://syddanskuni-my.sharepoint.com/:u:/g/personal/vgor_bmb_sdu_dk/EfUTZtwWt29Bn5nyvZd9y4UBbp3rPnnREVtqcqdDpleheA?e=KchRpA

[jorainer]

Looks good - at least, no problem reading that with the packages of the current Bioconductor release (3.15):

library(Spectra)
sps <- Spectra("small.mzML", source = MsBackendMzR())
spectraData(sps)
DataFrame with 48 rows and 34 columns
      msLevel     rtime acquisitionNum scanIndex            dataStorage
    <integer> <numeric>      <integer> <integer>            <character>
1           1    0.2961              1         1 /home/jo/tmp/mzR/iss..
2           1    0.4738              2         2 /home/jo/tmp/mzR/iss..
...       ...       ...            ...       ...                    ...
47          2   28.3862             47        47 /home/jo/tmp/mzR/iss..
48          2   29.2342             48        48 /home/jo/tmp/mzR/iss..
                dataOrigin centroided  smoothed  polarity precScanNum
               <character>  <logical> <logical> <integer>   <integer>
1   /home/jo/tmp/mzR/iss..       TRUE        NA         1          NA
2   /home/jo/tmp/mzR/iss..       TRUE        NA         1          NA
...                    ...        ...       ...       ...         ...
47  /home/jo/tmp/mzR/iss..       TRUE        NA         1          43
48  /home/jo/tmp/mzR/iss..       TRUE        NA         1          43
    precursorMz precursorIntensity precursorCharge collisionEnergy
      <numeric>          <numeric>       <integer>       <numeric>
1            NA                 NA              NA              NA
2            NA                 NA              NA              NA
...         ...                ...             ...             ...
47      558.900             198394               0              35
48      882.535             279259               0              35
    isolationWindowLowerMz isolationWindowTargetMz isolationWindowUpperMz
                 <numeric>               <numeric>              <numeric>
1                       NA                      NA                     NA
2                       NA                      NA                     NA
...                    ...                     ...                    ...
47                 557.900                 558.900                559.900
48                 881.535                 882.535                883.535
    peaksCount totIonCurrent basePeakMZ basePeakIntensity ionisationEnergy
     <integer>     <numeric>  <numeric>         <numeric>        <numeric>
1         1810      15245068    810.415           1471974                0
2         1598      12901166    810.546            183839                0
...        ...           ...        ...               ...              ...
47         659        100616    579.269           13265.4                0
48         636         77939    751.391           13049.5                0
        lowMZ    highMZ mergedScan mergedResultScanNum mergedResultStartScanNum
    <numeric> <numeric>  <integer>           <integer>                <integer>
1     202.608   1999.78         NA                  NA                       NA
2     200.134   1999.58         NA                  NA                       NA
...       ...       ...        ...                 ...                      ...
47    166.270   1127.58         NA                  NA                       NA
48    251.112   1743.36         NA                  NA                       NA
    mergedResultEndScanNum injectionTime           filterString
                 <integer>     <numeric>            <character>
1                       NA        68.227 FTMS + p ESI Full ms..
2                       NA         2.077 ITMS + p ESI Full ms..
...                    ...           ...                    ...
47                      NA        83.052 ITMS + c ESI d Full ..
48                      NA        86.348 ITMS + c ESI d Full ..
                spectrumId ionMobilityDriftTime scanWindowLowerLimit
               <character>            <numeric>            <numeric>
1   controllerType=0 con..                   NA                  200
2   controllerType=0 con..                   NA                  200
...                    ...                  ...                  ...
47  controllerType=0 con..                   NA                  140
48  controllerType=0 con..                   NA                  230
    scanWindowUpperLimit
               <numeric>
1                   2000
2                   2000
...                  ...
47                  1130
48                  1780

so, seems mzR version 2.30.0 contains already a proteowizard version which is able to read these files.

[caetera]

@jorainer , I have released the new version today, thus, I suggest closing the issue.