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 <[email protected]> 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: [email protected] > [mailto:[email protected]] On Behalf Of Bio X2Y > Sent: Tuesday, October 25, 2011 1:10 PM > To: [email protected] > 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 > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to > [email protected]<mailto:[email protected]> . > To unsubscribe from this group, send email to > [email protected]<mailto:spctools-discuss+unsub > [email protected]>. > For more options, visit this group > athttp://groups.google.com/group/spctools-discuss?hl=en. > > ________________________________ > > UT Southwestern Medical Center > The future of medicine, today. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
