Can you predict how well a peptide will ionize and fragment in HCD?

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Angiotensin Member
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Can you predict how well a peptide will ionize and fragment in HCD?

Postby Jen_G » Sun Apr 14, 2013 8:00 am

Hi All
I am thinking of spiking in a heavy K labeled peptide into my sample that will be dimethyl labeled. I am hoping that I can use a peptide that will be carried through my purification so I can use it to normalize at the end. Is there a way to ensure that I design a sequence than can be readily seen in the mass spec? I am using a Q-Exactive.

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E. Coli Lysate Member
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Postby Doug » Sun Apr 14, 2013 10:07 am

Hi Jen,

There are a lot of ways to approach this problem. If you want a tryptic peptide you could check out PeptideAtlas. It is a database of identified peptides (for several organisms). You can just enter your peptide sequence and see how many times it has been identified.

A lot of work has been put into algorithms for SRM to choose peptides that are unique to proteins and detectable. My guess is that software packages such as Skyline have features to predict how observable a peptide sequence is. But I don't have any experience with this.
"If we knew what we were doing it wouldn't be research." -AE

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