Spectra

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Bug in filterPrecursorScan()

4

```r > library(rpx) > PXD022816 (mzmls sp sp2 length(sp2) [1] 12 ``` ```r spectraData(sp2)[, c("msLevel", "acquisitionNum", "precScanNum", "dataOrigin")] ``` | msLevel| acquisitionNum| precScanNum|dataOrigin | |-------:|--------------:|-----------:|:----------------------------------------------------| | 1| 2479| NA|207e04bccd3dd_QEP2LC6_HeLa_50ng_251120_01-calib.mzML |...

lgatto

Function to find/visualise contaminants

2

In PR #259, I included a message about mz being sorted. As pointed by @sgibb, we haven't done so in other instances, and I suppose it doesn't bring much anyway...

lgatto

pickPeaks fails to centroid if no flanking zeroes are present

4

Hi there! While working with raw LC-IM-MS data (related to https://github.com/sneumann/xcms/pull/647), I've noticed that `pickPeaks` does not correctly centroid the data if no flanking zero values are present. Concretely, it...

RogerGinBer

filterPrecursorMzRange

2

DDA MS/MS defines the precursor that was used to trigger the MS/MS event, and defines the precursor mass as the trigger mass. However, every MS/MS event has a mass isolation...

cbroeckl

Export Spectra as HDF5 format (.h5)?

6

Hi, I'd like to ask if there's currently a way to write out a `Spectra` S4 object, probably initially read as `.mzML` or `.mzXML`, as `.h5`? There doesn't seem to...

Don86

This question came up during the review for PR #247 : Should we restrict the `spectraData` and `spectraData

jorainer

compareSpectra limits using joinPeaksGnps

4

Hi, I was testing the GNPS functionality from MsCoreUtils with `compareSpectra`. However, when I have a lot of MS2 spectra to compare (1603 MS2), it seems that computational limits are...

LiesaSalzer

Down-sampling spectra

3

I would like to down-sample spectra in order to know if I am close to reaching saturation of proteins identified in a sample. First I would like to know if...

cutleraging

Allow transformations when "joinPeaks'

1

It was nice to talk with you at the MetaRbolomics hackathon 2021. The idea of this issue is to allow/detect some fixed mass difference between peaks when joining them. This...

mengchen18

filterPrecursorMz with multiple precursor m/z values

1

At present `filterPrecursorMz` expects a range of m/z values and keeps all spectra with a precursor m/z within that range. I'm wondering if it would not also be nice to...

jorainer