@@Confess_Tsaki As far as I have understood, finding out the exact length of the peaks in this situation would be extremely difficult. You could calculate where the peaks are by looking at the bonds of the compound as well as how strong these bonds are. (For example the double bond in CO2 makes it strong, which is the reason why it does not fragment very often compared to propane) This information could help you figure out where the peaks are as well as approximating their length. But to get more exact than that I believe you need to do an actual mass spectrograph and check from that... That is everything I know on the topic, but please keep in mind that I am fairly new to it as well so there might be something obvious I am missing!
de novo peptide sequencing/ bottom up approach LC-MS-CID-MS/ CID: collision induced dissociation/ de novo peptide sequencing interpration algorithms & empirical rules/ de novo peptide sequencing machine learning programs
this helps sm, i have an exam tmrw and i didnt even touch my chem books once the whole semester. this is one of the only topics i thought was straight up nonsense, your vid clears it up thank you
This is the best channel I have ever come across, and I have discovered that it is far better than gold in my opinion i appreciate everything you have done for us
@@LucasLearnz Thank you, Lucas! Could you create a video on how to think of innovative research ideas that go beyond demographic studies? I’m always amazed by Japanese researcher university i feel so little and their publications-they come up with such groundbreaking ideas that leave me wondering how they even think of them!
I have a question: so on the right is the whole peptide who isn't separated into smaller ions? On left you have the peptide who is separeerde into different options of the peptide, so you get different ion formations. and these ions are extually amino acids?
Hello. Please how can I explain the rationale behind the buffer gas pressure difference between simulation (0.3 mTorr) and experimental conditions (approximately 5 Torr and 2.8 mTorr) in a linear ion trap
It has to do with how many particles hit the detector simultaneously. So if CO2 is analysed it’s mostly broken down to CO so therefore there will be a large spike in the 28 molecular weight position. Does that answer your question?😇
Great video thanks. One question...if we look at m/z 191 for example, which is triterpanes as far as I remember, we see many peaks from C21 or so up to C37 or so..now, all those peaks from ~C21 to ~C37 are fragments that give off a m/z 191 fragmentation when going through the ionization, am I correct? But the main molecules would have a mass of ~296 (C21) up to 520(C37), also correct?
@@LucasLearnz but then how will we know what the fragment is? Let's assume there is a peak at 50, this can come from directly 50 (+1 charge) or 100 devided by 2 (+2 charge). Then how does it work? I am kind of confused 😕
If I understand your question correctly, the device should display the relative length of the peaks as well... These were just pictures I found online to use as general examples. Hopefully that helps!
How do you actually determine the charge state of an ion in mass spectrometry. I mean, I know how the mass is determined. For example by TOF, quadruple etc. Is the charge of an ion determined by how far it is deflected by the magnetic field in the mass spectrometer? Hope my question is clear, thanks a lot
To the best of my understanding, which to be fair is limited, the charge is always either plus or minus 1. This is a requirement for the spectrometry to work. How that is ensured however, I am not certain about... I apologize, I cannot be of more help!
@@LucasLearnz I found it out in the mean while :) It can be concluded based on the mass/charge ratio which you obtain in the spectrum. You have to look at the mass/charge ratios between individual peaks of the ion fragment/precursor and calculate back to the charge. So, if the difference between the m/z of 2 peaks is for example 0.3, the charge would be +3. If it is 0.5 the charge is +2 and if it’s 1 the charge of the fragment/precursor is also 1. It is calculated by taking the reciprocal of the difference in m/z. E.g., if the difference between to peaks is 0.3 then the charge is 1/0.3=3, if the difference is 0,5 then the charge is 1/0,5=2 Thanks for your time and answer!
@@noraspeiser1865 Yeah, that was the impression I got as well when reading about MALDI in preparation for the video! But okay, that makes sense thank you so much once more, really appreciate you taking the time to share your knowledge with me!
What should I cover next?🤔
how do we know the length of those peaks more especially on compounds??
Let’s take they give you a compound and they tell you to draw mass spectrometry peaks from sketch
@@Confess_Tsaki As far as I have understood, finding out the exact length of the peaks in this situation would be extremely difficult. You could calculate where the peaks are by looking at the bonds of the compound as well as how strong these bonds are. (For example the double bond in CO2 makes it strong, which is the reason why it does not fragment very often compared to propane) This information could help you figure out where the peaks are as well as approximating their length. But to get more exact than that I believe you need to do an actual mass spectrograph and check from that...
That is everything I know on the topic, but please keep in mind that I am fairly new to it as well so there might be something obvious I am missing!
de novo peptide sequencing/ bottom up approach LC-MS-CID-MS/ CID: collision induced dissociation/ de novo peptide sequencing interpration algorithms & empirical rules/ de novo peptide sequencing machine learning programs
@@emdm00011000 Thank you so much for the suggestions! Will add it to my video topics list!
this helps sm, i have an exam tmrw and i didnt even touch my chem books once the whole semester. this is one of the only topics i thought was straight up nonsense, your vid clears it up thank you
Super happy to hear that!😇❤️
This is the best channel I have ever come across, and I have discovered that it is far better than gold in my opinion i appreciate everything you have done for us
That is so kind of you! Thank you so much!
@@LucasLearnz Thank you, Lucas! Could you create a video on how to think of innovative research ideas that go beyond demographic studies? I’m always amazed by Japanese researcher university i feel so little and their publications-they come up with such groundbreaking ideas that leave me wondering how they even think of them!
why didn't this channel exist when I was doing my bachelor's 15 years ago!!!! very helpful
That's so nice of you! Thank you!!🙏🙏
Thanks!
Thank you! You don't have to do that🙈♥️ But thank you so much! Let me know if I can help you out in some other way😇
Thank you for the effort you put into these videos :D
Thank you for showing your appreciation! Makes me genuinely happy!
You are amazing! Thank you, brilliant work, very helpful!
That is so nice of you! Thank you so much! Happy I could help!😇👍
Thank you for making this video! I'm pretty sure you just saved me from failing my exam tomorrow!
I hope your exam went well!👍👍
How it was?
@@Helio_Gaitabad of course. It's always bad
Nice explanation Lucas thanks!
I''m happy I was able to help!😀
Amazing lecture
Just love the teaching style❤
Really helpful😊
Where can you access these databases to compare your spectra?
Well explained👏
That's very kind of you and makes me happy to hear that!😇👍
CO2 has double bonds between C and O
I have a question: so on the right is the whole peptide who isn't separated into smaller ions? On left you have the peptide who is separeerde into different options of the peptide, so you get different ion formations. and these ions are extually amino acids?
Are there any free databases of mass spec? I’m actually having a hard time right now in my PhD with a tough load of mass spec
thank you so much!! very helpful!!!
I'm very happy I could help!😇👍
Does the abundance have to be the same in the two graphs for them to be considered a match?
I must admit I'm not entirely sure but to my understanding they don't have to be exactly the same.
thank you so much for your help 💜💜
You're very welcome!😇
thank you so much this was very helpful.
Glad to help😇👍
Hello. Please how can I explain the rationale behind the buffer gas pressure difference between simulation (0.3 mTorr) and experimental conditions (approximately 5 Torr and 2.8 mTorr) in a linear ion trap
Do u have any other mass spectroscopy explanation videos??...
why height of y axis differ?
It has to do with how many particles hit the detector simultaneously.
So if CO2 is analysed it’s mostly broken down to CO so therefore there will be a large spike in the 28 molecular weight position.
Does that answer your question?😇
Great video thanks. One question...if we look at m/z 191 for example, which is triterpanes as far as I remember, we see many peaks from C21 or so up to C37 or so..now, all those peaks from ~C21 to ~C37 are fragments that give off a m/z 191 fragmentation when going through the ionization, am I correct? But the main molecules would have a mass of ~296 (C21) up to 520(C37), also correct?
I have GC graphs and MS graphs, so how do I identify unknown sample.
thanks for the explanation!
Thanks for watching!
Thanks for explanation
Excellent to hear that the video was helpful!👍
Excellent, thanks!
You're very welcome😇👍
Thank you. Finally understood, didnt have to pour over a book
Fantastic to hear! So happy that I could help!
What if the fragment has +2 charge? Then the m/z ratio is divided by 2?
Correct!👍
@@LucasLearnz but then how will we know what the fragment is? Let's assume there is a peak at 50, this can come from directly 50 (+1 charge) or 100 devided by 2 (+2 charge). Then how does it work? I am kind of confused 😕
How will we know there abundances
How do we know the length of the peaks for a compound let's take...
If I understand your question correctly, the device should display the relative length of the peaks as well... These were just pictures I found online to use as general examples. Hopefully that helps!
Very nice. Thank you.
That's so nice of you! Thank you!
How do you actually determine the charge state of an ion in mass spectrometry. I mean, I know how the mass is determined. For example by TOF, quadruple etc. Is the charge of an ion determined by how far it is deflected by the magnetic field in the mass spectrometer?
Hope my question is clear, thanks a lot
To the best of my understanding, which to be fair is limited, the charge is always either plus or minus 1. This is a requirement for the spectrometry to work. How that is ensured however, I am not certain about... I apologize, I cannot be of more help!
@@LucasLearnz
I found it out in the mean while :)
It can be concluded based on the mass/charge ratio which you obtain in the spectrum. You have to look at the mass/charge ratios between individual peaks of the ion fragment/precursor and calculate back to the charge. So, if the difference between the m/z of 2 peaks is for example 0.3, the charge would be +3. If it is 0.5 the charge is +2 and if it’s 1 the charge of the fragment/precursor is also 1. It is calculated by taking the reciprocal of the difference in m/z.
E.g., if the difference between to peaks is 0.3 then the charge is 1/0.3=3, if the difference is 0,5 then the charge is 1/0,5=2
Thanks for your time and answer!
@@noraspeiser1865 Thank you so much for sharing that answer! I am trying to learn and get better at this stuff too!
@@LucasLearnz in MALDI ionization the charge is always plus 1, here we don't need to think about it. Only in ESI we need to consider the charge
@@noraspeiser1865 Yeah, that was the impression I got as well when reading about MALDI in preparation for the video! But okay, that makes sense thank you so much once more, really appreciate you taking the time to share your knowledge with me!
thanks a lot
I'm happy I could help!
Thx!
Thank you for watching!
I love you.
Thank you! I'm happy I could help!😇👍