Thanks a lot for these videos. However, a doubt remains. The peptic fragments are just being blasted with inert gas to break them down into b and y ions. Where from are the extra 1 or rather 2 H+ at the N terminal of 'y-ions' coming from, giving them overall +1 charge?
The peptide ions are accelerated into the collision cell and collide with the inert gas molecules, which causes the fragmentation. There are no extra H+. The peptide starts out 2H+ and the fragments are 1H+.
This was very helpful but I still have one question. I don't get why the relative intensities of complementary b and y fragments are different, like b2 and y10 in your example. I mean, when the parent ion fragments on a specific bond you get the same amount of the two complementary fragments, so I really don't get this. could you help me please?
Hey sir! Thanks for the help- question I had is how would you draw a simple mechanism for the y and b fragmentation? How do both the nitrogen np oxygen become positively charged? Thanks for the vid!
@@MatthewPadula How does that scheme account for the first b ion? according to that you would never get a N-terminal single amino acid, would always have at least two side-chains incorporated
@@erikhenze2339 b1 is the singly charged parent ion mass minus the largest y-ion. With CID you probably will see b1 but not a lot more of the b-series. This depends on the amount of peptide. I don't understand about the side-chains comment.
I have a questions I did all this, b ions I got sequence of RYAAYKYA and for y ions I have the sequence of IKAYKYAA I am not sure what's my final sequence going to be
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You're a legend! This is currently helping me with my mass spec lab in my biochemistry degree 💪🏽📊
Super great! Thank you very much. It is very helpful to me, a beginner of MS user
This saved my skin, thank you so much! Succinct and easy to understand.
This video was really a life-saver. Thank you!!!
This Video is extremely helpful, thank you so so much!
Thank you for your kind explanation :) This is very helpful
This was very helpful! Thank you!
Just the information i needed! Thank you sir :)
Thanks a lot for these videos. However, a doubt remains.
The peptic fragments are just being blasted with inert gas to break them down into b and y ions.
Where from are the extra 1 or rather 2 H+ at the N terminal of 'y-ions' coming from, giving them overall +1 charge?
The peptide ions are accelerated into the collision cell and collide with the inert gas molecules, which causes the fragmentation. There are no extra H+. The peptide starts out 2H+ and the fragments are 1H+.
This was very helpful but I still have one question. I don't get why the relative intensities of complementary b and y fragments are different, like b2 and y10 in your example. I mean, when the parent ion fragments on a specific bond you get the same amount of the two complementary fragments, so I really don't get this. could you help me please?
Excellent!
Hey sir! Thanks for the help- question I had is how would you draw a simple mechanism for the y and b fragmentation? How do both the nitrogen np oxygen become positively charged? Thanks for the vid!
link.springer.com/article/10.1007/s13361-016-1341-0 - see scheme 6
@@MatthewPadula How does that scheme account for the first b ion? according to that you would never get a N-terminal single amino acid, would always have at least two side-chains incorporated
@@erikhenze2339 b1 is the singly charged parent ion mass minus the largest y-ion. With CID you probably will see b1 but not a lot more of the b-series. This depends on the amount of peptide. I don't understand about the side-chains comment.
this is really informative video, thank you so much, can we have the ppt version i want to study it as well
I have a questions I did all this, b ions I got sequence of RYAAYKYA
and for y ions I have the sequence of IKAYKYAA
I am not sure what's my final sequence going to be
You did all of what? Is it a tryptic peptide? If so, it should end in K or R. You should probably email me with more detailed info.
@@MatthewPadula Hi, Please i urgently need help, where do i find your email?
Its fine found it, I am going to send you an email right now thanks a lot!!!
@@FunTime-hd4zz searching my name and "UTS" in Google is a good start.
Really appreciate it, I have sent the email! 🙂