Content-Type: multipart/alternative; boundary="_000_CE5463239184FA4FACFB29AEF551E2E153A5B2WEXMBX1Awcmcqnet_" --_000_CE5463239184FA4FACFB29AEF551E2E153A5B2WEXMBX1Awcmcqnet_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello Marc, Mathias, and whoever is supporting ProteoWizard. Apologies for asking you directly for help; I couldn't find a suitable help= forum to ask on. Let me know if there is some other place I should be ask= ing for this. I created an mz5 file from a Thermo raw file using ProteoWizard, and I'm ha= ving a little trouble understanding what is contained in the SpectrumMZ ele= ment. I'm trying to draw spectrograms of intensity vs. m/z. Here's a sample of w= hat I see in Xcalibur: [cid:image001.png@01CF8EF4.0FF62DF0] Here's the same scan after I convert to mz5 and import it into R: [cid:image002.png@01CF8EF4.98C44E00] The intensity values contained in the SpectrumIntensity element are what I = expected, but the m/z values are way too low. That is, I was expecting tha= t the values would mainly be in the 100 to 1300 range but they are actually= mostly between 0.01 and 0.04. I guess that SpectrumMz contains values in some other unit (though they are= not linearly related to the expected m/z values in Thompsons), but I can't= find any mz5 documentation or ProteoWizard documentation that explains wha= t that unit might be. Please can you tell me what SpectrumMz contains, and how I might convert th= ose values to Thompsons. Many thanks. Regards, Richie WCMC-Q --_000_CE5463239184FA4FACFB29AEF551E2E153A5B2WEXMBX1Awcmcqnet_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello Marc, Mathias, and whoever is supporting Prote= oWizard.

 

Apologies for asking you directly for help; I couldn= 't find a suitable help forum to ask on.  Let me know if there is some= other place I should be asking for this.

 

I created an mz5 file from a Thermo raw file using P= roteoWizard, and I'm having a little trouble understanding what is containe= d in the SpectrumMZ element.

 

I'm trying to draw spectrograms of intensity vs. m/z= .  Here's a sample of what I see in Xcalibur:

 

 

Here's the same scan after I convert to mz5 and impo= rt it into R:

 

The intensity values contained in the SpectrumIntens= ity element are what I expected, but the m/z values are way too low.  = That is, I was expecting that the values would mainly be in the 100 to 1300= range but they are actually mostly between 0.01 and 0.04.

 

I guess that SpectrumMz contains values in some othe= r unit (though they are not linearly related to the expected m/z values in = Thompsons), but I can't find any mz5 documentation or ProteoWizard document= ation that explains what that unit might be.

 

Please can you tell me what SpectrumMz contains, and= how I might convert those values to Thompsons.

 

Many thanks.

 

Regards,

Richie

 

WCMC-Q

 

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