From Where In The Mzml File Does Toppview Get The Retention Time?

Question

[Niek De Klein]

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

Answer 1

[Laurent]

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.

[Niek De Klein]

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