Query: RES for sulfate ions and DBA

[Clendinen, Chaevien S]

Hello,

 

My colleagues are very excited to use this software for our research. We have run into a few issues with its utilization however, we are attempting to use the GlycReSoft software to create a search space for polysulfated glycans. We are not able to find the RES for sulfate or sulfite ions (see for xylose pasted below), and dibutylamine, the ion pairing agent we use for the LC

 

"names": [

"Xylose",

"Xyl"

],

"structure": "RES 1b:x-dxyl-PEN-1:5"

},

 

Thank you for your help, look forward to hearing from you

 

____________________________________

Chaevien S. Clendinen, Ph.D

Chemist

Biosystem Dynamics & Simulation Group

Environmental Molecular Sciences Laboratory (EMSL)

Pacific Northwest National Laboratory (PNNL)

902 Battelle Boulevard

P.O. Box 999, MSIN K8-98

Richland, WA 99352 USA

Office: EMSL-2568

Tel: 509-375-2381

Email: Chaevien....@pnnl.gov  

www.emsl.pnnl.gov

www.pnnl.gov

 

[Joshua Klein]

Hello,

If your goal is to add an unlocalized sulfate substituent to a monosaccharide, you can use the name "sulfate" or "@sulfate" in the combinatorial generator table and the algorithm will include 0-n SO3 groups to the total glycan composition. If you are composing a text file to be imported, then including "sulfate" or "@sulfate" as a composition component will have the same effect. I haven't dealt with sulfite before but I assume because it is a radical it will react more readily, but still only lead to a net gain of SO3 for the modified glycan.

If you do not want to express SO3 as a component of a glycan composition but as a variable adduct, you can instead specify it at search time. Assuming you are using released glycans, it would look something like this:

This would lead to the search engine treating glycans with and without these modifications as the same entity for the purposes of scoring and quantification.

As a pure glycoinformatics aside, in GlycoCT, you express sulfation as a substituent, which means it is its own node in the table:

RES
1b:x-dxyl-PEN-1:5
2s:sulfate
LIN
1:1o(4+1)2n

While this is quite explicit, it is also verbose. IUPAC expresses the equivalent as ?-D-Xylp4S or Xyl3S (or even XylS). GlycReSoft will understand XylS in the context of glycan compositions, though any of these representations work for the underlying glypy library. 

Does this answer your question?

Thank you,

Joshua Klein

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Joshua Klein

[Clendinen, Chaevien S]

Hi,

 

Thank you for your prompt response. Is there any advice on the dibutylamine substituents?

 

Chaevien

 

From: Joshua Klein <jak...@bu.edu>
Sent: Wednesday, May 25, 2022 6:06 PM
To: Clendinen, Chaevien S <chaevien....@pnnl.gov>
Cc: glycr...@googlegroups.com; Attah, Kwame <kwame...@pnnl.gov>; Berger, Madelyn R <madelyn...@pnnl.gov>
Subject: Re: Query: RES for sulfate ions and DBA

 

Check twice before you click! This email originated from outside PNNL.

 

Hello,

 

If your goal is to add an unlocalized sulfate substituent to a monosaccharide, you can use the name "sulfate" or "@sulfate" in the combinatorial generator table and the algorithm will include 0-n SO3 groups to the total glycan composition. If you are composing a text file to be imported, then including "sulfate" or "@sulfate" as a composition component will have the same effect. I haven't dealt with sulfite before but I assume because it is a radical it will react more readily, but still only lead to a net gain of SO3 for the modified glycan.

 

If you do not want to express SO3 as a component of a glycan composition but as a variable adduct, you can instead specify it at search time. Assuming you are using released glycans, it would look something like this:

[Joshua Klein]

I'm not familiar with dibutylamine and how it'd behave in this circumstance. Is it a reducing end modification (in which case you can specify it as the reducing end formula), or can it appear at any hydroxyl group in any number of occurrences on a monosaccharide? If you want to express it as an unplaced composition component, you can write it as "#dibutylamine#C8H19NO-1H-1" in either the text file composition specification or as a row in the combinatorial hypothesis table.

 

The reducing end formula may need to have an extra hydrogen added to it as it opens the reducing end monosaccharide's carbon backbone ring. 

The "#<name>#<formula>" notation can accept any formula you want to enter, but the algorithm can't do anything intelligent with it beyond adding it to the chemical composition and mass of each glycan. Also, please verify whether the dibutylamine replaces the hydroxyl group (hence the O-1H-1 added to the formula), or if it bonds with the hydroxyl group's oxygen and just drops the hydrogen (H-1 then).

In either case, if you're using some sort of charge-boosting reagent, you may want to configure the search to use the null charge feature:

This way, the scoring function doesn't try to apply an inappropriate classification rule when evaluating confidence.

--

Joshua Klein