Question: From Where In The Mzml File Does Toppview Get The Retention Time?
2
gravatar for Niek De Klein
5.8 years ago by
Niek De Klein2.4k
Netherlands
Niek De Klein2.4k wrote:

This question is related to my other question: http://biostar.stackexchange.com/questions/17403/how-can-i-get-the-retention-time-of-an-ms-ms-precursor-out-of-a-mzml-file-using-p).

I want to know where in an mzml file I can find the retention time of a spectrum. I have tried looking in the mzml file myself but have not found it. When opening an mzml file in TOPPView it shows the spectrums on a 2D plot with m/z as y-axis and retention time as x-axis, so it must be somewhere in the file. However, using ViM to search in the mzml file for a retention time as shown on TOPPView does not give any results.

From what or where in the mzml file does TOPPView get the retention times?

Thanks, Niek

• 1.4k views
ADD COMMENTlink written 5.8 years ago by Niek De Klein2.4k
4
gravatar for Laurent
5.8 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

Checking one of my own mzML files, the retention time corresponds to

<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.16391166666666665" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>

which make sense according to the data you presented in your previous question. I have also checked the values in the mzML file with those imported using mzR (which in turn uses the proteowizard library), and they match.

ADD COMMENTlink written 5.8 years ago by Laurent1.6k

Ah, it's in minutes, that's why I didn't recognize it. Thanks.

ADD REPLYlink written 5.8 years ago by Niek De Klein2.4k
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