1 Overview

GlycoAnnotateR is an R package for data-base free annotation of glycan compositions in mass spectrometry data. The package is designed to be flexible and work with many different types of mass spectrometry data (e.g. LC-MS, MALDI, direct injection), as well as the output of many different data processing pipelines (e.g. XMCS, Cardinal). Please see the tutorial for detailed explanations and instructions.

2 Installation

This package can be installed directly from Github using devtools:

library(devtools)
devtools::install_github('margotbligh/GlycoAnnotateR')

Please note that python is required for the package to function. If you do not have a local version of python available, please follow instructions to download and install.

3 Prediction parameters

The ‘prediction’ or ‘calculation’ of glycan compositions is the core utility of this package. Therefore a detailed description of the arguments is provided here.

3.1 Glycan composition parameters

Degree of polymerisation, dp

This is always a range from the lowest to highest DP desired (e.g. c(1,10) for DPs from 1 to 10)- if you need only a single DP, provide that DP twice (e.g. c(2,2) for only DP 2).
Should pentose be included in addition to hexose, pent_option

This is a logical argument for whether pentose monomers should be included in compositions in addition to hexose monomers.
Maximum number of modifications per monomer on average, nmod_max

Calculated by the number of modifications over the number of monomers. Does not take into account unsaturated, alditol or dehydrated. For example, for a tetramer (DP4) of deoxyhexoses with four sulfate groups, the average number of modifications per monomer is 2. By default nmod_max is 1, and the maximum allowed value is 3. Consider carefully whether you need to increase this value above the default.
Label, label

Are sugars labelled by reductive amination? Current supported labels are none (default) and those givin in the table below:

Label	Accepted names
procainamide	“procainamide”, “proca”, “procA”, “ProA”
2-aminopyridine	“2-ap”, “2-AP”, “pa”, “PA”, “2-aminopyridine”
2-aminobenzoic acid	“2-aa”, “2-AA”, “aba”, “ABA”, “2-aminobenzoic acid”
2-aminobenzamide	“2-ab”, “2-AB”, “ab”, “AB”, “2-aminobenzamide”
1-phenyl-3-methyl-5-pyrazolone	“pmp”, “PMP”, “1-phenyl-3-methyl-5-pyrazolone”

Double sulfate, double_sulfate

Can monomers be disulfated? Logical option required. To work sulfate must be in modifications and nmod_max at least 2.
Glycan linkage, glycan_linkage

By default none. When oglycan or nglycan the limits described by Cooper et al. (2021) for the GlycoMod software are implemented. Rules are listed here: https://web.expasy.org/glycomod/glycomod-doc.html
Modification limits, modification_limits

User provided limits on monomers or modifications. Provide as a named list.
Modifications, modifications

By default, each modification can occur once per monomer, and it is possible to have all modifications selected present on one monomer. After calculation of modified monomers they are filtered by the nmod_max term before output is returned. So, for example, for modifications = c('deoxy', 'sulfate', 'carboxylicacid'), the program will generate as one possible composition all three modifications on one monomer (i.e. ‘DeoxyHex1 CarboxylicAcid1 Sulfate1’). If nmod_max is at the default 1, this composition will be filtered out before output is returned (as the nmod = 3). Sulfate is the only modification which is allowed to occur twice per mononer. For this, you need to set double_sulfate=TRUE and nmod_max to be at least 2.

The different modifications and their namings are summarised below:

Modification	Definition / description	IUPAC naming	GlycoCT naming	Oxford naming
carboxylicacid	Effective loss of two hydrogens and gain of one oxygen to form a carboxylic acid group on C6. The modified monomer is commonly called a ‘uronic acid’	CarboxylicAcid	COOH	A
sialicacid	Effect addition of C11H19N1O9 to hexose. Here, sialic acid only refers to N-Acetylneuraminic acid (Neu5Ac), the most common sialic acid. Predominantly found in complex mammalian glycans.	NeuAc	SIA	SA
phosphate		Phosphate	PO4	P
sulfate	Addition of SO3. Only modification allowed to occur twice per monomer (see options for `double_sulfate`)	Sulfate	SO4	S
amino	Gain of NH and loss of of O - result ofreplacing a hydroxyl group with an amino group.	Amino	NH2	Am
deoxy	One hydroxyl group is replaced by an H atom. Fucose and rhamnose are two common deoxyhexoses. NB: GlycoAnnotateR currently only considers deoxyhexoses and not deoxypentoses.	DeoxyHex	DHEX	D
nacetyl	Addition of an N-acetyl group (net change = +C2H3N) . Common example of N-acetylated hexose is N-acetylglucosamine. Note that here, N-acetylglucosamine would be termed in e.g. IUPAC naming Hex1 N-Acetyl1.	N-Acetyl	NAc	N
oacetyl	Acetylation of a hydroxyl group (net change = +C2H2O).	O-Acetyl	Ac	Ac
omethyl	Addition of CH2 to an hydroxyl group. Natural modification, but can also be generated by permethylation.	O-Methyl	OMe	M
anhydrobridge	Water loss formed by bridge between two hydroxyl groups. Occurs from C6 to C3, C2 or C1. Seen in e.g. carrageenans.	AnhydroBridge	ANH	B
unsaturated	Water loss to form a C-C double bond inside a ring. Seen for example in ulvans and are the target of polysaccharide lyases.	Unsaturated	UNS	U
dehydrated	Water loss that occurs during ionisation or other reactions.	Dehydrated	Y	Y
alditol	Reducing end monomer is opened and the aldehyde reduced to an alcohol. Commonly done before PGC-LC to reduce anomer splitting of peaks. Refers to an alditol ‘modification’ not a monomer here.	Alditol	ALD	o
aminopentyllinker	Functional group used in synthetic chemistry. Can occur once per composition.	NH2Pent1	NH2Pent1	NH2Pent1

3.2 Mass spec parameters

Scan range, scan_range

Scan range (m/z) used during acquisition. For prediction/computation purposes only this can be set very wide. Compositions with no adduct with an m/z value inside the scan range will be filtered out.
Polarity, polarity

Negative (neg) and/or positive (pos) ionisation polarity used during acquisition. Changes the adducts returned. See below for specific adducts generated.
Ionisation type, ion_type

ESI (ESI) and/or MALDI (MALDI) ionisation used. Changes the adducts returned (MALDI has only singly charged ions, ESI can have multiply charged). See below for specific adducts generated.

3.3 Output and other parameters

Naming, naming

How should compositions be named? Options are IUPAC, GlycoCT and Oxford. As only compositions and not structures are given, conventions could not be followed closely, but common abbreviations from the conventions are used (see modifications table above).
Adducts, adducts

Options are: H, Na, NH4, K, Cl and CHOO. The adducts generated depends on adducts, polarity and ion type. The resulting adducts are summarised in the table below:

__NB: n is the number of anionic groups. Where relevant, ions will be generated with n values from 2-n. For example, in negative mode with MALDI and Na adducts, for a composition with four sulfate groups (n = 4) the adducts will include [M-2H+1Na]^-, [M-3H+2Na]^- and [M-4H+3Na]^-.

Adduct	Ion type	Polarity	Adducts generated
H	ESI	Positive	[M+H]⁺
		Negative	[M-H]^-, [M-nH]^-n
	MALDI	Positive	[M+H]⁺
		Negative	[M-H]^-
Na	ESI	Positive	[M+Na]⁺, [M-nH+(n+1)Na]⁺
		Negative	[M-nH+(n-1)Na]^-
	MALDI	Positive	[M+Na]⁺, [M-nH+(n+1)Na]⁺
		Negative	[M+nH+(n-1)Na]^-
NH4	ESI	Positive	[M+NH4]⁺, [M-nH+(n+1)NH4]⁺
	MALDI	Positive	[M+NH4]⁺, [M-nH+(n+1)NH4]⁺
		Negative	[M-nH+(n-1)NH4]^-
K	ESI	Positive	[M+K]⁺, [M-nH+(n+1)K]⁺
	MALDI	Positive	[M+K]⁺, [M-nH+(n+1)K]⁺
		Negative	[M-nH+(n-1)K]^-
Cl	ESI	Negative	[M+Cl]^-
	MALDI	Negative	[M+Cl]^-
CHOO	ESI	Negative	[M+CHOO]^-
	MALDI	Negative	[M+CHOO]^-

GlycoAnnotateR

Margot Bligh

2024-03-06