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-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 -- 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:[email protected]>. For more options, visit this group at http://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.
