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I've recorded high resolution fragmentation spectra (120k resolution) on the eclipse using the 'full profile' mode (s/n threshold on the orbi is set to 0). However, when I try to deconvolute this data…
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I'm working with MRM data aquired on a Waters instrument and exported into a .mzML format. I try to import them using xcms using the `readMSData()` function with no luck:
```
fls chr
```
…
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Laurent, do you know what governs the choice of number for the acquisitionNum in the mzR header()?
As some of the native ID formats contains multiple integer values this is important to ensure correc…
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Following this tutorial (https://jorainer.github.io/xcmsTutorials/articles/xcms-preprocessing.html#data-visualization), it would be nice to have a Galaxy tool that can create the plots of the small se…
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Hi there,
A couple things tripped up the code while I was running a fragpipe workflow that included PTM Shepherd analysis:
At the end of an otherwise smooth analysis, I was repeatedly getting th…
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Hi
I'm having an error with PTMShepherd with reading my mzML files on linux.
```
PTMShepherd [Work dir: /data/MS_2024-10-01-001/finalDB_MBR_3ppm3minRT_10topRuns_0.5cor/out]
java -Xmx490G -Dlib…
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I recently updated to R version 4.1.1 and updated XCMS and associated packages to 3.14.1. Using Waters MSe data, I have previously successfully using findChromPeaks for both MS1 and MS2 using the add=…
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Full disclosure: We have an instrument that may be having some issues.
That said, I have looked at this data, and I have not found zero-variance rows or columns in the dataMatrix (when substituting…
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mzR support mzXML and mzdata formats - it would be nice to also implement the package to natively be able to deal with those formats.
This should be implemented in this function: https://github.com/R…
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Hi,
I recently run into installation error, please see the error message and session below. It only concerns macos, neither on windows nor on linux.
I've updated `mzR` and `bioconductor`, unf…