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More than one glycosylation site #160
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If you are using the glyco workflow, MSFragger-glyco can only detect one glycosylation per peptide, unless you change the mass offsets list to contain the masses equal the summation of multiple glycosylations. In that case, you MIGHT be able to see some peptides with multiple glycosylation, but you will have to do the "deconvolution" by yourself because MSFragger-Glyco only reports the total masses of the glycosylations. Best, Fengchao |
Are you looking for multiple glyco sites in a single peptide, or on a whole protein? As Fengchao said, we currently can only identify a single mass shift per peptide (which can be the summed mass of glycans on multiple sites), but we cannot currently break down the mass into individual sites, though we are working on adding a way to do this in the future. |
Thank you for the quick response! I am asking for a single peptide - I had
run the search with O-Pair and Byonic before, and I know a couple of
peptides that have more than one glycosite. Thanks for letting me know!
…On Tue, Jun 15, 2021 at 11:24 AM Daniel Polasky ***@***.***> wrote:
Are you looking for multiple glyco sites in a single peptide, or on a
whole protein? As Fengchao said, we currently can only identify a single
mass shift per peptide (which can be the summed mass of glycans on multiple
sites), but we cannot currently break down the mass into individual sites,
though we are working on adding a way to do this in the future.
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With N-liked, the changes of getting 2 sites (with two NxS/T motifs) on the same peptide are quite low.
Are you doing O-linked glyco? Yes, we are currently assigning it as a single mass shift on one residue, even though some may actually be 2 different glycans. But we do not have that functionality like in O-pair yet.
Alexey
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Sent: Tuesday, June 15, 2021 11:34 AM
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Subject: Re: [Nesvilab/MSFragger] More than one glycosylation site (#160)
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Thank you for the quick response! I am asking for a single peptide - I had
run the search with O-Pair and Byonic before, and I know a couple of
peptides that have more than one glycosite. Thanks for letting me know!
…On Tue, Jun 15, 2021 at 11:24 AM Daniel Polasky ***@***.***<mailto:***@***.***>> wrote:
Are you looking for multiple glyco sites in a single peptide, or on a
whole protein? As Fengchao said, we currently can only identify a single
mass shift per peptide (which can be the summed mass of glycans on multiple
sites), but we cannot currently break down the mass into individual sites,
though we are working on adding a way to do this in the future.
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.
--
Valentina Rangel Angarita (They/She)
PhD Student - Malaker Lab
https://www.malakerlab.com/
Department of Chemistry
Yale University
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Hello, Thank you for any information, Hans |
Hi Hans, We do not currently have an option for HCD-only localization of multiple labile modifications on a peptide given the challenges in doing so, but you can still identify the peptide and total mass of modifications using a labile search. |
Dear Dan, thank you for the quick response. |
Hi Hans, Best, |
Dear Dan, |
The current version of FragPipe has O-pair localization module that supports multiple O-glycans. I think this issue can be considered as resolved. Best, Fengchao |
I've run a couple of searches with MSFragger - Glyco, and I have noticed that it only identifies one glycosylation site (despide increasing the number of possible modifications). Is there any way to change this? I know my sample should have 1-3 glyco sites based on other searches done in other programs.
Thanks!
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