MS/MS tolerance of instruments

[Fengchao]

Dear all,

I always not quite sure in setting MS/MS tolerances for different instrument. As far as I know, QE can be set to 0.02 for sure. What about LTQ Orbitrap Velos and LTQ Orbitrap Elite? I checked their manuals. They are all provide a very high resolution and mass accuracy. Take LTQ Orbitrap Velos for example:

However, there people suggest treat LTQ Orbitrap MS/MS as low resolution and set the tolerance to 1.0005. Then, I am confused. Could somebody provide some advise?

Thanks

[Jimmy Eng]

The proper fragment ion settings in Comet depends on the mass analyzer used to acquire the MS/MS data.  For the two instruments you mentioned, both of them have two mass analyzers.  So you can acquire MS/MS in either the Orbitrap or in the ion trap (LTQ or Velos) of these instruments.  This means the MS/MS data can be either high resolution or lower resolution.  It more common that the MS/MS spectra are acquired in the ion trap analyzers of these instruments hence the suggested low resolution settings.  However, if you know that the MS/MS spectra were acquired in the Orbitrap then you would use the high resolution settings.  Hope this makes sense; please follow up if this isn't clear.

[Fengchao]

Thanks for your detailed reply! Then, I have another question: how to identify the type of mass analyzer from the mzXML file (or raw if I have Xcalibur). I paste the instrument information in a mzXML file in the below. Is this means that it is a high resolution MS/MS?

  <msInstrument>

   <msManufacturer category="msManufacturer" value="Thermo Scientific" />

   <msModel category="msModel" value="LTQ Orbitrap" />

   <msIonisation category="msIonisation" value="NSI" />

   <msMassAnalyzer category="msMassAnalyzer" value="FTMS" />

   <msDetector category="msDetector" value="unknown" />

   <software type="acquisition" name="Xcalibur" version="2.2 SP1" />

  </msInstrument>

Thanks

[Paulo C Carvalho]

If you have the Xcalibur the easiest way is opening the file in the viewer.  Verify an MS1 (Full MS) mass spectrum on qual browser.  On my example below it reads FTMS, meaning it was obtained in the Orbitrap.

My MS2 ( Full ms2) was obtained in the LTQ (ITMS).

Remember that even if data is acquired in hi-res fore MS1 to use some broad search window to narrow results later in a filtering step.

Right-click on the spectrum, view->intrument method will also provide you with details on the method as reflected below.

I suggest searching the results directly from the RAW files not to keep generating extra files on your disk, besides, repos will accept the raw files.

Cheers,

Paulo

--

Paulo Costa Carvalho

http://pcarvalho.com

[Fengchao]

Dear Paulo,

Thank you very much for you detailed answer. Now, I have no further question.

Thanks,

Fengchao