MS/MS Peptide Identification - Please Clarify “Monoisotopic vs Average” Parameter

[Bio X2Y]

Hi,

(I posted the following question to BioStar several days ago, where it hasn't received a reply. Hopefully someone here can help. http://biostar.stackexchange.com/questions/13406/ms-ms-peptide-identification-please-clarify-monoisotopic-vs-average-parameter)

Both Mascot and X!Tandem offer a parameter for "monoisotopic vs average" (X!Tandem calls it "spectrum, fragment mass type"). Even after reading the documentation, I'm unclear on the meaning of this parameter - perhaps someone can clarify?

In general, I understand the difference between MS1 and MS2 scans, and I understand the existence of isotope envelopes at both MS1 and MS2 levels. I'm also clear on the point that the first peak (all-12C) of an isotope envelope is the monoisotopic peak, which may or may not be the most intense peak.

My best guess regarding the parameter (although I'm not at all confident): both engines assume that you have de-isotoped your MS2 spectra before submission, and that this parameter is asking the user to clarify whether the deisotoping procedure retained the monoisotopic peak or the most intense peak.

Thanks for your time.

X!Tandem explanation: http://www.thegpm.org/TANDEM/api/sfmt.html

Mascot explanation: http://www.matrixscience.com/help/search_field_help.html#MASS

[David Trudgian]

See:

 

http://ionsource.com/tutorial/isotopes/slide8.htm

 

for a good explanation.

 

DT

 

--

David Trudgian Ph.D.

Instructor, Biochemistry Dept and Proteomics Core

UT Southwestern Medical Center at Dallas

6001 Forest Park Rd, Dallas, TX 75390-8816

Room:ND6.214 Tel:(214)648-7025 Fax:(214)645-6298

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[bio.x2y]

Hi David,

Thanks for the link, it is a nice illustration of the difference
between monoisotopic and average masses.

However, what I'm hoping to find out is what the monoisotopic vs
average parameter means in the context of a peptide identification
program like Mascot or X!Tandem. e.g.

Possible Interpretation 1 - setting the parameter to "monoisotopic"
means that you are telling Mascot that your MS2 spectra have already
been peak-picked/deisotoped prior to submission, and that the peak-
picking procedure you used identified monoisotopic peaks rather that
an average-mass peaks for the isotope envelopes.

Possible Interpretation 2- setting the parameter to "monoisotopic"
means that your as expecting Mascot to de-isotope your MS2 spectra for
you (i.e. the spectra you submit contain all peaks for each isotope),
and that you're confident that your data is high-enough resolution for
Mascot to attempt to identify the monoisotopic peaks rather than
average-mass peaks for the purpose of comparison to theoretical
spectra.

Thanks.

On Oct 25, 10:36 pm, David Trudgian

<David.Trudg...@UTSouthwestern.edu> wrote:
> See:
>
> http://ionsource.com/tutorial/isotopes/slide8.htm
>
> for a good explanation.
>
> DT
>
> --
> David Trudgian Ph.D.
> Instructor, Biochemistry Dept and Proteomics Core
> UT Southwestern Medical Center at Dallas
> 6001 Forest Park Rd, Dallas, TX 75390-8816
> Room:ND6.214 Tel:(214)648-7025 Fax:(214)645-6298
>
> From: spctools...@googlegroups.com [mailto:spctools...@googlegroups.com] On Behalf Of Bio X2Y
> Sent: Tuesday, October 25, 2011 1:10 PM
> To: spctools...@googlegroups.com
> Subject: [spctools-discuss] MS/MS Peptide Identification - Please Clarify “Monoisotopic vs Average” Parameter
>
> Hi,
>

> (I posted the following question to BioStar several days ago, where it hasn't received a reply. Hopefully someone here can help.http://biostar.stackexchange.com/questions/13406/ms-ms-peptide-identi...)

>
> Both Mascot and X!Tandem offer a parameter for "monoisotopic vs average" (X!Tandem calls it "spectrum, fragment mass type"). Even after reading the documentation, I'm unclear on the meaning of this parameter - perhaps someone can clarify?
>
> In general, I understand the difference between MS1 and MS2 scans, and I understand the existence of isotope envelopes at both MS1 and MS2 levels. I'm also clear on the point that the first peak (all-12C) of an isotope envelope is the monoisotopic peak, which may or may not be the most intense peak.
>
> My best guess regarding the parameter (although I'm not at all confident): both engines assume that you have de-isotoped your MS2 spectra before submission, and that this parameter is asking the user to clarify whether the deisotoping procedure retained the monoisotopic peak or the most intense peak.
>
> Thanks for your time.
>
> X!Tandem explanation:http://www.thegpm.org/TANDEM/api/sfmt.html
> Mascot explanation:http://www.matrixscience.com/help/search_field_help.html#MASS
>
> --
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> To post to this group, send email to spctools...@googlegroups.com<mailto:spctools...@googlegroups.com> .
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