In ESI, with a single pure proteofrom being ionised, each peak will represent a different charge state of the protein, with a smaller m/z being a higher charge state (more H+ attached). To work out the mass of the protein, simultaneous equations can be used and this can be done manually with enough time. Software that comes with the MS often does this, but there is also online calculators like this one: www.bioprocess.org/esiprot/esiprot_form.php.
I have a question about the difference in m/z values between peptides containing the C-12 or C-13 isotopes for isotopes - and this has driving me slightly insane for a bit because I encountered the same problem while reading a paper as well - at 5:08, when you go through the calculation of the m/z value for the peptide containing the C-13 isotope - why did you add the mass value of 1 Da corresponding to the one extra neutrino just once? Because this would mean that there is only one C-13 atom in the entire peptide, whereas, I thought all the carbon atoms in "isotopic peptide" would be the C-13 isotopes and therefore the mass of the "isotopic peptide" would be much larger due to the many extra neutrinos present there. Is my interpretation incorrect? When people refer to the peptide containing the C-13 isotope do they mean that there is only one C-13 carbon atom present in the peptide? Would be extremely grateful for a clarification, thanks!
In nature, C13 is ~1% of all of the carbon atoms available (that number isn't exact, but whatever). In a peptide, each carbon atom in the peptide has a 1% chance of being C13. A peptide has 10-1000's of carbon atoms depending on its length and the chance of one of them being C13 is 1% for each position, so it is highly likely that a single molecule of a peptide has at least one C13. Because different molecules of the same peptide can have a C13 at different locations in the molecule, those molecules will have the same m/z in a MS1 scan. It would be extremely rare that all of the carbons in a single molecule of a naturally occurring peptide would be C13. Then you need enough of these molecules of exactly the same thing to detect. So you would detect the molecules with no C13's first because they are the most abundant, then those with one C13, then those with 2 C13's etc as the abundance of those molecules of the same peptide sequence get less and less.
Bwahahahahahahaha! No, I'm not a smoker. But the audio was recorded at about 7am in my office by myself with a headset. I realise that I need to be more dynamic.
Four years and someone finally picks up a 'mistake'. You tell me what the common name for an uncharged ion is, one that is able to enter the MS, be past through the instrument and able to strike the detector, giving a false signal? An uncharged molecule, I guess.
Hello Dr. I will like to know if you have a published paper concerning this overview because I will like to use it as one of my references for a research paper I'm writing on "Translational Proteomics with Advanced Mass Spectrometry (MS) Systems".
This is all out of my own head using articles and text books that were already out there, along with discussions with engineers. So I don't have a single article. If you email me, I'll try and find some srticles to send you.
This is a great summary but there are some serious copyright infringement issues with this video. The simulations in the LC-MS are straight from Thermo Scientific. There is no credit attributed to Thermo anywhere in the video and it is not clear that permission has been given for use of their video.
Somebody please get this guy a glass water.
THANK YOU
I can't even focus on what he's saying because all I hear are those wet mouth noises that melt my brain
Jesus Christ 🙏😂
😂😂😂😂😂
Makes it unwatchable, unfortunately
A comprehensive overview of Mass spectrometry.
Good job Matthew.
This is absolutely AMAZING. Thank you and please make more videos science needs you.
Every protein man deserves such an ultimate perfect instruction.
Took me a while to find this explanation. Perfect overview of the subject.
Great video! I learned a lot, thank you for the hard work.
Best explanation I saw. Congrats!
Very great explanation! Thanks- now I get an idea of how mess spectrometry works for biomolecules.
Very well done! great amount of info for under 30 min.
fukken brilliant m8. thanks a lot for the detailed intro.
Thank you! You are so good at explaining honestly.
Thanks Matthew, this great material!!
Thank you so much! I needed this for my uni course.
Bloody legend mate
Thank you so much, I definitely owe you one 👏🙌
Thank you!!!!
thanks so much
This is a general theoretical on mass spectrometry. Would be more useful if top-down and bottom-up approaches in proteomics were covered.
Yes. It is on the to-do list. Hopefully in the next few weeks, these will start to be updated. They take a long time to get done properly.
Brilliant but good lord it sounds like you're presenting to the Top 30 CEOs of the Fortune 500. Get some water homie.
You don't like the sexy huskiness? ;)
Great video, but this guy needs to take some pauses in between!
thank you for uploading
elaborate explanation
thank you so much!!!
How can one determine the molecular mass of protein by the peaks given in graph?
In ESI, with a single pure proteofrom being ionised, each peak will represent a different charge state of the protein, with a smaller m/z being a higher charge state (more H+ attached). To work out the mass of the protein, simultaneous equations can be used and this can be done manually with enough time. Software that comes with the MS often does this, but there is also online calculators like this one: www.bioprocess.org/esiprot/esiprot_form.php.
I have a question about the difference in m/z values between peptides containing the C-12 or C-13 isotopes for isotopes - and this has driving me slightly insane for a bit because I encountered the same problem while reading a paper as well - at 5:08, when you go through the calculation of the m/z value for the peptide containing the C-13 isotope - why did you add the mass value of 1 Da corresponding to the one extra neutrino just once?
Because this would mean that there is only one C-13 atom in the entire peptide, whereas, I thought all the carbon atoms in "isotopic peptide" would be the C-13 isotopes and therefore the mass of the "isotopic peptide" would be much larger due to the many extra neutrinos present there. Is my interpretation incorrect? When people refer to the peptide containing the C-13 isotope do they mean that there is only one C-13 carbon atom present in the peptide? Would be extremely grateful for a clarification, thanks!
In nature, C13 is ~1% of all of the carbon atoms available (that number isn't exact, but whatever). In a peptide, each carbon atom in the peptide has a 1% chance of being C13. A peptide has 10-1000's of carbon atoms depending on its length and the chance of one of them being C13 is 1% for each position, so it is highly likely that a single molecule of a peptide has at least one C13. Because different molecules of the same peptide can have a C13 at different locations in the molecule, those molecules will have the same m/z in a MS1 scan.
It would be extremely rare that all of the carbons in a single molecule of a naturally occurring peptide would be C13. Then you need enough of these molecules of exactly the same thing to detect. So you would detect the molecules with no C13's first because they are the most abundant, then those with one C13, then those with 2 C13's etc as the abundance of those molecules of the same peptide sequence get less and less.
Right, that makes a lot of sense, thanks for the context!
HOW DID YOU IDENTIFIED THESE ARE ISOTOPES OF CARBON
Cheers!
Great information, thank you, but kindly are you a smoker Dr?
Bwahahahahahahaha! No, I'm not a smoker. But the audio was recorded at about 7am in my office by myself with a headset. I realise that I need to be more dynamic.
@@MatthewPadula oh great, I just thought you had breathing difficulty, I would not even be speaking that early and again thank you for the videos. 😊
@16:46 What the heck is an "uncharged ion"????????
Four years and someone finally picks up a 'mistake'. You tell me what the common name for an uncharged ion is, one that is able to enter the MS, be past through the instrument and able to strike the detector, giving a false signal? An uncharged molecule, I guess.
Hello Dr.
I will like to know if you have a published paper concerning this overview because I will like to use it as one of my references for a research paper I'm writing on "Translational Proteomics with Advanced Mass Spectrometry (MS) Systems".
This is all out of my own head using articles and text books that were already out there, along with discussions with engineers. So I don't have a single article. If you email me, I'll try and find some srticles to send you.
like and subscribed 👍
This is a great summary but there are some serious copyright infringement issues with this video. The simulations in the LC-MS are straight from Thermo Scientific. There is no credit attributed to Thermo anywhere in the video and it is not clear that permission has been given for use of their video.
Pffft
go from the simple thing, don't mix the stafs
The Thermo video (ruclips.net/video/KjUQYuy3msa/видео.html) is no longer available.
Remind me where this is referred to in the video.
@@MatthewPadula 20:17
@@SethCrosby Thanks. I will fix it for the next version.
Myoglobin 11:35
dada
deeeeeeeyta you say, huh?