Update CVs, add `electronBeamEnergy` #311

Adafede · 2025-08-14T05:53:21Z

ran updateCvParams.sh properly this time

jorainer · 2025-08-19T07:08:55Z

Quick question: was there already a "electronBeamEnergy" header variable before or did you add one? Seems you simply moved the header variable to a different position?

Adafede · 2025-08-19T07:41:37Z

@jorainer It was already listed there, indeed, at the end and while adding in https://github.com/sneumann/mzR/pull/311/files#diff-463c44a6d90a9e18b0f360386960d386888894194c952be75b24d60196577ebbR27 for example, it felt more intuitive to place it next to the CID energy?

jorainer · 2025-08-19T07:48:00Z

ah, yes, of course. Makes more sense. I was just confused, because if you would have added a new header variable you would also need to increment the size of the vector/list - otherwise you run into a nullpointer.

jorainer

Please add also unit tests to check that the electroBeamEnergy header is set.

Also, I got a bit puzzled by the ms-obo version - seems you are replacing the existing one with an older version?

src/pwiz/data/common/psi-ms.obo

Adafede · 2025-08-19T13:01:05Z

Please add also unit tests to check that the electroBeamEnergy header is set.

Happy to, but this would require an mzML with electroBeamEnergy in it? Shall I fake one/add it to msdata? Just need some guidance on how you would like this one at best and happy to implement it

jorainer · 2025-08-19T13:19:32Z

honestly - I would for now just check that the variable is returned - by the netCDF and the pwiz - and that the values are (presumably?) NA. If you happen to have your own mzML files with that electroBeamEnergy you could just report here that they are correctly extracted (maybe show the first x lines of the header() output).

Adafede · 2025-08-19T13:29:19Z

Oh, yes, absolutely I can confirm that! I already converted thousands of files using my own branch and get the electronBeamEnergy 😄 maybe @Panzenboeck can also confirm?

(Mainly did it for Adafede/CentroidR#6)

Adafede · 2025-08-19T13:33:48Z

Here a file with CID only:

<precursorList count="1">
            <precursor>
              <isolationWindow>
                <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="100.075376300915" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
              </isolationWindow>
              <selectedIonList count="1">
                <selectedIon>
                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="100.075376300915" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
                </selectedIon>
              </selectedIonList>
              <activation>
                <cvParam cvRef="MS" accession="MS:1000422" name="beam-type collision-induced dissociation" value=""/>
                <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="40.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
              </activation>
            </precursor>
          </precursorList>

and with EAD:

<precursorList count="1">
            <precursor>
              <isolationWindow>
                <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="795.725926070743"/>
              </isolationWindow>
              <selectedIonList count="1">
                <selectedIon>
                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="795.725926070743" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="0.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
                </selectedIon>
              </selectedIonList>
              <activation>
                <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
                <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="12.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
                <cvParam cvRef="MS" accession="MS:1003294" name="electron activated dissociation" value=""/>
                <cvParam cvRef="MS" accession="MS:1003410" name="electron beam energy" value="16.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
              </activation>
            </precursor>
          </precursorList>

(with still a small CID current for transmission)

Panzenboeck · 2025-08-19T15:05:09Z

@Adafede, yes, I can confirm that I also get the electronBeamEnergy and I highly recommend CentroidR!

jorainer · 2025-08-20T06:21:21Z

Thanks for the update @Adafede - for the two example files that you show above, can you maybe show what mzR::header() returns for these?

Adafede · 2025-08-20T08:00:10Z

Sure!

library(mzR)
#> Loading required package: Rcpp
path_cid <- "Downloads/20230912_nexus_plate_1_Q1_pos_A1_CID_20ev.mzML"
path_ead <- "Downloads/20230912_nexus_plate_1_Q1_pos_A1_EAD_16KE.mzML"
path_cid_mini <- "Downloads/mini_cid.mzmL"
path_ead_mini <- "Downloads/mini_ead.mzmL"

range <- 1L:5L

## Switch to the mini solution if no access to the large original file
if (!path_cid |>
  file.exists()) {
  print("using mini example")
  path_cid <- path_cid_mini
}
if (!path_ead |>
  file.exists()) {
  print("using mini example")
  path_ead <- path_ead_mini
}

in_file_cid <- path_cid |>
  mzR::openMSfile(backend = "pwiz")
in_file_ead <- path_ead |>
  mzR::openMSfile(backend = "pwiz")

hdr_cid <- in_file_cid |>
  mzR::header()
hdr_ead <- in_file_ead |>
  mzR::header()

pks_cid <- in_file_cid |>
  mzR::peaks()
pks_ead <- in_file_ead |>
  mzR::peaks()

in_file_cid |>
  mzR::close()
in_file_ead |>
  mzR::close()

hdr_cid_mini <- hdr_cid[!hdr_cid$collisionEnergy |> is.na(), ][range, ]
hdr_cid_mini$seqNum <- range
hdr_ead_mini <- hdr_ead[!hdr_ead$collisionEnergy |> is.na(), ][range, ]
hdr_ead_mini$seqNum <- range

pks_cid_mini <- pks_cid[!hdr_cid$collisionEnergy |> is.na()][range]
pks_ead_mini <- pks_ead[!hdr_ead$collisionEnergy |> is.na()][range]

print(hdr_cid_mini)
#>    seqNum acquisitionNum msLevel polarity peaksCount totIonCurrent
#> 21      1             21       2        1        872     58107.316
#> 22      2             22       2        1       1361     25404.693
#> 24      3             24       2        1       1158     34536.109
#> 25      4             25       2        1        256      4207.717
#> 27      5             27       2        1        919     11382.867
#>    retentionTime basePeakMZ basePeakIntensity collisionEnergy
#> 21         2.075          0                 0              20
#> 22         2.133          0                 0              20
#> 24         2.307          0                 0              20
#> 25         2.364          0                 0              20
#> 27         2.539          0                 0              20
#>    electronBeamEnergy ionisationEnergy lowMZ highMZ precursorScanNum
#> 21                 NA                0     0      0               NA
#> 22                 NA                0     0      0               NA
#> 24                 NA                0     0      0               NA
#> 25                 NA                0     0      0               NA
#> 27                 NA                0     0      0               NA
#>    precursorMZ precursorCharge precursorIntensity mergedScan
#> 21    107.0464               0                  0         NA
#> 22    155.0720               0                  0         NA
#> 24    132.9587               0                  0         NA
#> 25    608.7878               0                  0         NA
#> 27    131.1037               0                  0         NA
#>    mergedResultScanNum mergedResultStartScanNum mergedResultEndScanNum
#> 21                  NA                       NA                     NA
#> 22                  NA                       NA                     NA
#> 24                  NA                       NA                     NA
#> 25                  NA                       NA                     NA
#> 27                  NA                       NA                     NA
#>    injectionTime filterString                              spectrumId
#> 21             0         <NA> sample=1 period=1 cycle=20 experiment=2
#> 22             0         <NA> sample=1 period=1 cycle=20 experiment=3
#> 24             0         <NA> sample=1 period=1 cycle=21 experiment=2
#> 25             0         <NA> sample=1 period=1 cycle=21 experiment=3
#> 27             0         <NA> sample=1 period=1 cycle=22 experiment=2
#>    centroided ionMobilityDriftTime isolationWindowTargetMZ
#> 21      FALSE                   NA                107.0464
#> 22      FALSE                   NA                155.0720
#> 24      FALSE                   NA                132.9587
#> 25      FALSE                   NA                608.7878
#> 27      FALSE                   NA                131.1037
#>    isolationWindowLowerOffset isolationWindowUpperOffset scanWindowLowerLimit
#> 21                         NA                         NA                   50
#> 22                         NA                         NA                   50
#> 24                         NA                         NA                   50
#> 25                         NA                         NA                   50
#> 27                         NA                         NA                   50
#>    scanWindowUpperLimit
#> 21                 1500
#> 22                 1500
#> 24                 1500
#> 25                 1500
#> 27                 1500
print(hdr_ead_mini)
#>    seqNum acquisitionNum msLevel polarity peaksCount totIonCurrent
#> 21      1             21       2        1       1480      22693.71
#> 22      2             22       2        1       1266      16772.92
#> 24      3             24       2        1       1332      20061.95
#> 25      4             25       2        1        961      10115.71
#> 27      5             27       2        1       1266      16157.14
#>    retentionTime basePeakMZ basePeakIntensity collisionEnergy
#> 21         2.096          0                 0              12
#> 22         2.184          0                 0              12
#> 24         2.388          0                 0              12
#> 25         2.476          0                 0              12
#> 27         2.679          0                 0              12
#>    electronBeamEnergy ionisationEnergy lowMZ highMZ precursorScanNum
#> 21                 16                0     0      0               NA
#> 22                 16                0     0      0               NA
#> 24                 16                0     0      0               NA
#> 25                 16                0     0      0               NA
#> 27                 16                0     0      0               NA
#>    precursorMZ precursorCharge precursorIntensity mergedScan
#> 21    250.9533               0                  0         NA
#> 22    483.1817               1                  0         NA
#> 24    155.1042               0                  0         NA
#> 25    398.3646               0                  0         NA
#> 27    152.9503               0                  0         NA
#>    mergedResultScanNum mergedResultStartScanNum mergedResultEndScanNum
#> 21                  NA                       NA                     NA
#> 22                  NA                       NA                     NA
#> 24                  NA                       NA                     NA
#> 25                  NA                       NA                     NA
#> 27                  NA                       NA                     NA
#>    injectionTime filterString                              spectrumId
#> 21             0         <NA> sample=1 period=1 cycle=20 experiment=2
#> 22             0         <NA> sample=1 period=1 cycle=20 experiment=3
#> 24             0         <NA> sample=1 period=1 cycle=21 experiment=2
#> 25             0         <NA> sample=1 period=1 cycle=21 experiment=3
#> 27             0         <NA> sample=1 period=1 cycle=22 experiment=2
#>    centroided ionMobilityDriftTime isolationWindowTargetMZ
#> 21      FALSE                   NA                250.9533
#> 22      FALSE                   NA                483.1817
#> 24      FALSE                   NA                155.1042
#> 25      FALSE                   NA                398.3646
#> 27      FALSE                   NA                152.9503
#>    isolationWindowLowerOffset isolationWindowUpperOffset scanWindowLowerLimit
#> 21                         NA                         NA                   50
#> 22                         NA                         NA                   50
#> 24                         NA                         NA                   50
#> 25                         NA                         NA                   50
#> 27                         NA                         NA                   50
#>    scanWindowUpperLimit
#> 21                 1500
#> 22                 1500
#> 24                 1500
#> 25                 1500
#> 27                 1500

mzR::writeMSData(file = path_cid_mini, header = hdr_cid_mini, object = pks_cid_mini)
mzR::writeMSData(file = path_ead_mini, header = hdr_ead_mini, object = pks_ead_mini)

^{Created on 2025-08-20 with reprex v2.1.1}

With the mini examples in case here below
mini_examples.zip

jorainer

Thanks @Adafede for adding support for this spectra variable! I'm OK with the C++ and R code - for the OBO and CV terms I would like to have @sneumann a look (as well as to merge as he's the maintainer).

sneumann

Looks good to me. For the psi-ms I created a shell-script many years back to perform the update, and Adriano now has confirmed that it still works :-) Also, the perceived downgrade of psi-ms.obo makes sense.
Yours, Steffen

src/pwiz/data/common/psi-ms.obo

sneumann · 2025-08-20T10:34:37Z

What is missing is the contributor in the DESCRIPTION file...

Adafede · 2025-08-20T12:30:37Z

So...after some additional checks...

you might want to check your... checks
https://github.com/sneumann/mzR/actions/runs/16992490191/job/48175088324#step:20:274 is failing but is 🟢
tests are failing because of https://github.com/sneumann/mzR/pull/311/files#diff-26f099db195730ac5bdeb078040629190bbc6a1dd0129a53cfe8f1bd2d3f2761R805-R817, which ends up as some columns "missing" (altough they were not there at the beginning, they were just articially added "empty"). I can also remove the "remove NaNs part" of this PR but it feels weird that mzR creates additional lines. This is related to Generated mzMLs contain value="nan" instead of value="NaN" #307
- in case I have a downstream fix in Adafede/CentroidR@5456e1b

Happy to hear your thoughts @jorainer

sneumann#311 (comment)

jorainer · 2025-08-21T07:24:28Z

as far as I understand you are skipping to WRITE missing/NaN values back to the mzML file - which makes total sense to me! I would keep it like that - but then update/fix the unit tests for that.

why the unit tests fail but are still green is a very odd... maybe related to RUnit instead of testthat... no clue.

jorainer · 2025-09-02T11:34:21Z

We are now getting bunch of errors in Spectra and MSnbase - because the export() does not work - the header validator in mzR cries that no electronBeamEnergy is available in the submitted header. I would maybe like to change the electronBeamEnergy to be an optional, but not required field? Is that OK @Adafede ?

Adafede · 2025-09-02T11:37:43Z

@jorainer Absolutely! Please let me know when done so that I can remove my ugly temporary fix in https://github.com/Adafede/CentroidR/blob/main/R/centroid_one_file.R#L335-L350 😊

(I believe all of these could be optional)

Make electronBeamEnergy an optional header column for export

jorainer · 2025-09-03T05:35:46Z

Update: @sneumann , we fixed now the failing unit tests (see results from unit tests here) and importantly also fixed an issue that causes both the MSnbase and Spectra packages to fail with the current mzR: we made the electronBeamEnergy an optional header column for the export functionality.

sneumann · 2025-09-03T12:33:12Z

Thanks, merged and pushed to BioC. Yours, Steffen

Adafede changed the title ~~Update CVs~~ Update CVs, add electronBeamEnergy Aug 14, 2025

jorainer requested changes Aug 19, 2025

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jorainer requested review from jorainer and sneumann August 20, 2025 08:26

jorainer approved these changes Aug 20, 2025

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sneumann approved these changes Aug 20, 2025

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Update DESCRIPTION

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sneumann#311 (comment)

Merge remote-tracking branch 'adafede/devel' into adafede

3c9edb0

jorainer and others added 3 commits September 2, 2025 15:29

refactor: make electronBeamEnergy an optional header column

ff6dbf1

fix unit test

57c02f0

Merge pull request #1 from jorainer/adafede

15fde15

Make electronBeamEnergy an optional header column for export

sneumann merged commit 15fde15 into sneumann:devel Sep 3, 2025
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Update CVs, add electronBeamEnergy #311

Update CVs, add electronBeamEnergy #311

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Update CVs, add `electronBeamEnergy` #311

Update CVs, add `electronBeamEnergy` #311

Adafede commented Aug 20, 2025 •

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