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IUPAC-Condensed Glycan Notation

Source: vignettes/articles/iupac.Rmd
iupac.Rmd

This article introduces IUPAC-condensed glycan notation, the main text format used by glyrepr for representing glycan structures. The goal is to show how a branched glycan structure can be written as a compact, readable string.

Why Are There So Many Glycan Formats?

Different communities have developed different ways to describe glycans, each optimized for a specific use case. Some formats are easy for people to read, some are better for databases and software, and others preserve detailed chemical information.

Let’s use one N-glycan as an example:

The same molecule can be written in several formats:

IUPAC-condensed:

Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-

IUPAC-extended:

α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)-β-D-GlcpNAc-(1→2)-α-D-Manp-(1→3)[α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)-β-D-GlcpNAc-(1→2)-α-D-Manp-(1→6)]-β-D-Manp-(1→4)-β-D-GlcpNAc-(1→4)[α-L-Fucp-(1→6)]-β-D-GlcpNAc-(1→

WURCS:

WURCS=2.0/6,12,11/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-3-1-4-5-3-1-4-5-6/a4-b1_a6-l1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f3-g2_h2-i1_i4-j1_j3-k2

InChI:

InChI=1S/C90H148N6O66/c1-21-47(116)59(128)62(131)81(142-21)140-20-40-69(55(124)43(77(135)143-40)93-24(4)108)152-78-44(94-25(5)109)56(125)66(36(16-103)148-78)153-82-63(132)72(156-86-76(61(130)51(120)33(13-100)147-86)158-80-46(96-27(7)111)58(127)68(38(18-105)150-80)155-84-65(134)74(53(122)35(15-102)145-84)162-90(88(138)139)9-29(113)42(92-23(3)107)71(160-90)49(118)31(115)11-98)54(123)39(151-82)19-141-85-75(60(129)50(119)32(12-99)146-85)157-79-45(95-26(6)110)57(126)67(37(17-104)149-79)154-83-64(133)73(52(121)34(14-101)144-83)161-89(87(136)137)8-28(112)41(91-22(2)106)70(159-89)48(117)30(114)10-97/h21,28-86,97-105,112-135H,8-20H2,1-7H3,(H,91,106)(H,92,107)(H,93,108)(H,94,109)(H,95,110)(H,96,111)(H,136,137)(H,138,139)/t21-,28-,29-,30+,31+,32+,33+,34+,35+,36+,37+,38+,39+,40+,41+,42+,43+,44+,45+,46+,47+,48+,49+,50+,51+,52-,53-,54+,55+,56+,57+,58+,59+,60-,61-,62-,63-,64+,65+,66+,67+,68+,69+,70+,71+,72-,73-,74-,75-,76-,77+,78-,79-,80-,81+,82-,83-,84-,85-,86+,89-,90-/m0/s1

Each format serves its purpose:

  • IUPAC formats: readable text formats for describing glycan structures.
  • WURCS/GlycoCT: structured formats designed for databases and software.
  • Semantic formats: formats designed for linking data across platforms.
  • Chemical formats: formats used for detailed chemical representation.

Why glyrepr Uses IUPAC-Condensed

When building glyrepr, we needed a native text format for glycan structures. IUPAC-condensed is a practical choice because it balances readability and information content.

  • Human-readable: structures can usually be interpreted without specialized software.
  • Information-rich: it captures the monosaccharides, branches, linkages, anomers, and substituents needed for many glycomics analyses.
  • Widely used: it is familiar to many researchers in the glycomics community.
  • Flexible: it can represent both simple and complex glycan structures.

For other formats such as WURCS or GlycoCT, the broader glycoverse workflow can use parser packages such as glyparse.

Reading IUPAC-Condensed Notation

Step 1: Monosaccharide Symbols

Every glycan is built from monosaccharide units, and IUPAC notation gives each one a short abbreviation:

Full Name Symbol
Galactose Gal
Glucose Glc
Mannose Man
N-Acetylglucosamine GlcNAc
Fucose Fuc

For a broader list of symbols, see the SNFG website or run available_monosaccharides().

IUPAC-condensed names normally omit absolute configuration and assume the natural form, such as L-fucose for Fuc and D-gulose for Gul. glyrepr writes a less common configuration with D- or L- before the residue name: D-Fuc, L-Gul, or D-Fucf for D-fucofuranose. The unprefixed natural names remain canonical; redundant forms such as L-Fuc and D-Gul are not accepted.

Step 2: Substituents

Glycans can contain chemical modifications called substituents. In IUPAC-condensed notation, substituents are written after the monosaccharide name.

  • Neu5Ac9Ac = a sialic acid with an extra acetyl group at position 9.
  • Glc3Me = a glucose with a methyl group at position 3.
  • GlcNAc6Ac = an N-acetylglucosamine with acetylation at position 6.

Format rule: Position number + Modification type
Example: 6Ac = “acetyl group at position 6”

Step 3: Linkage Information

Linkages tell us how monosaccharides are connected to each other.

The anatomy of a linkage:

MonosaccharideA(anomeric_config + anomeric_position - target_position)MonosaccharideB

For example, Neu5Ac(a2-3)Gal means:

  • Neu5Ac is connected to Gal
  • The anomeric carbon of Neu5Ac is in alpha configuration (a)
  • The connection is from position 2 of Neu5Ac
  • To position 3 of Gal

Sometimes not all linkage details are known, so we use ? as a wildcard:

  • a2-? = the anomer and donor position are known, but the acceptor position is unknown.
  • ??-3 = the acceptor position is known, but the anomer and donor position are unknown.

Step 4: Topological Structure

The main challenge in IUPAC-condensed notation is writing a branched tree as a linear string. Branches are placed in square brackets and inserted before the residue they attach to.

The basic rules are:

  1. Find the longest backbone
  2. Treat everything else as a branch
  3. Branches go in square brackets []
  4. Write branches just before the monosaccharide they connect to
  5. Apply the same rules recursively inside each branch

Example 1: A Simple O-Glycan

Step-by-step construction:

  1. Identify the main chain: Gal -> GlcNAc -> GalNAc
  2. Add linkage info: Gal(b1-4)GlcNAc(b1-6)GalNAc(a1-
  3. Spot the branch: The bottom Gal connects to GalNAc
  4. Insert the branch: Gal(b1-4)GlcNAc(b1-6)[Gal(b1-3)]GalNAc(a1-
  5. The branch is a single “Gal(b1-3)” unit, no need for step 5.

Final result:

Gal(b1-4)GlcNAc(b1-6)[Gal(b1-3)]GalNAc(a1-

Example 2: The N-Glycan Core

This example has two chains of equal length. The tie-breaker rule decides which one becomes the main chain.

IUPAC’s tie-breaker rule: When chains are equal, choose the one that creates branches with lower position numbers.

Analysis: - Option A: Man(a1-6) branch -> position 6 - Option B: Man(a1-3) branch -> position 3

Option B is chosen because 3 is lower than 6.

Final result:

Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-

Example 3:

This example is more complex: it has three branches with the same length, branching on different residues. In this case, we look for the first breaking point from right to left: the b4 Man. Two mannoses are connected to that Man, one with an a1-3 linkage and the other with an a1-6 linkage. According to the tie-breaker rule, we choose the a1-3 branch as the main chain. First, write the main chain:

Man(a1-2)Man(a1-2)Man(a1-3)[BRANCH]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-

Now look at the branch, which also contains its own branch.

Using the tie-breaker rule again, the branch can be written as:

BRANCH = Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-6)]Man(a1-6)

Combining the main chain and the branch gives:

Man(a1-2)Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-

Step 5: Reducing-End Anomeric Information

You might wonder: “Why does the last monosaccharide end with (b1- instead of a complete linkage?”

The root monosaccharide (rightmost) doesn’t connect to anything further, so its anomeric carbon is “free.” The format (xy- tells us about its anomeric state without a target.

An alditol is marked by adding -ol to the reducing-end residue while retaining the reducing-end annotation used by glyrepr, for example Gal(b1-4)GlcNAc-ol(a1-.

Floating Parts

Sometimes a substructure is known but its parent in the complete glycan is not. For example, a bi-antennary N-glycan may contain one sialic acid without enough evidence to determine which terminal galactose carries it.

glyrepr represents such a floating part in braces before the main IUPAC-condensed structure:

{Neu5Ac(a2-3)}<main glycan>

Omitting a parent list means that every feasible node outside the floating part’s own component is a candidate. To retain a known candidate set, add a pipe followed by comma-separated complete-sequence node indices:

{Neu5Ac(a2-3)|2,5}<main glycan>

The indices follow the left-to-right residue order of the complete IUPAC-condensed sequence: residues inside floating blocks are counted before the main glycan, while substituent blocks contribute no nodes. Thus the floating Neu5Ac above is node 1 and its candidate main-tree residues are nodes 2 and 5. The |2,5 suffix is a glyrepr extension to curly-brace IUPAC notation. A floating part may target a residue in another floating component, but not one in its own component. All selected component attachments must be acyclic and ultimately connect to the main tree.

For example, in {Gal(b1-4)|2,3}Glc(a1-3)Man(a1-, Gal is node 1 and may attach to Glc (node 2) or Man (node 3).

An explicit candidate set needs at least two nodes to remain floating. Singleton syntax is still accepted, but it fully localizes the attachment and is serialized as an ordinary linkage. For example, {Neu5Ac(a2-3)|2}Gal(b1-4)GlcNAc(b1- becomes Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-. Singleton localization is iterative, so attaching one floating component to another can resolve further domains.

Here is the complete bi-antennary example:

floating_n_glycan <- as_glycan_structure(
  paste0(
    "{Neu5Ac(a2-3)|2,5}",
    "Gal(b1-4)GlcNAc(b1-2)Man(a1-3)",
    "[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]",
    "Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"
  )
)
floating_n_glycan
#> <glycan_structure[1]>
#> [1] {Neu5Ac(a2-3)|2,5}Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> # Unique structures: 1
structure_floating_parts(floating_n_glycan)
#> # A tibble: 1 × 6
#>   glycan_id part_id root_node nodes     linkage parents  
#>       <int>   <int>     <int> <list>    <chr>   <list>   
#> 1         1       1         1 <int [1]> a2-3    <int [2]>

Floating blocks may contain more than one residue, and multiple blocks may precede the same main glycan. glyrepr canonicalizes their order while preserving duplicate floating parts and remapping every candidate-parent set to the resulting complete-sequence order. Floating substituents use the same global node domain and may therefore target residues in floating parts.

Practice

Challenge: Look at the complex N-glycan at the beginning of this article and try to write its IUPAC-condensed string yourself.

Hint: Start by identifying the main chain, then work on the branches one by one.

Test your answer:

# Try your hand-written string here!
my_attempt <- "Your_IUPAC_string_here"

# This will tell you if it's valid
tryCatch({
  result <- as_glycan_structure(my_attempt)
  cat("Your IUPAC string is valid.\n")
  print(result)
}, error = function(e) {
  cat("The string could not be parsed.\n")
  cat("Error:", e$message, "\n")
})
#> The string could not be parsed.
#> Error: In index: 1.

Summary

IUPAC-condensed notation is compact enough for routine analysis while still preserving the structural details that glyrepr needs. In this article, you saw:

  • why different glycan formats exist and when IUPAC-condensed is useful.
  • how to read monosaccharide symbols and substituents.
  • how linkage notation encodes anomeric configuration and positions.
  • how branched tree structures are converted into linear strings.
  • how main chains and branches are selected with tie-breaker rules.

Next steps:

  • Practice with more complex structures
  • Explore the glyrepr package functions
  • Use as_glycan_structure() to validate and work with IUPAC-condensed strings

Session Information 

sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.5 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] glyrepr_1.1.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] jsonlite_2.0.0    dplyr_1.2.1       compiler_4.6.1    tidyselect_1.2.1 
#>  [5] Rcpp_1.1.2        stringr_1.6.0     jquerylib_0.1.4   systemfonts_1.3.2
#>  [9] textshaping_1.0.5 yaml_2.3.12       fastmap_1.2.0     R6_2.6.1         
#> [13] generics_0.1.4    igraph_2.3.3      knitr_1.52        backports_1.5.1  
#> [17] checkmate_2.3.4   tibble_3.3.1      desc_1.4.3        bslib_0.12.0     
#> [21] pillar_1.11.1     rlang_1.3.0       utf8_1.2.6        cachem_1.1.0     
#> [25] stringi_1.8.9     xfun_0.61         fs_2.1.0          sass_0.4.10      
#> [29] otel_0.2.0        cli_3.6.6         pkgdown_2.2.1     magrittr_2.0.5   
#> [33] digest_0.6.39     lifecycle_1.0.5   vctrs_0.7.3       evaluate_1.0.5   
#> [37] glue_1.8.1        ragg_1.5.2        rmarkdown_2.32    purrr_1.2.2      
#> [41] tools_4.6.1       pkgconfig_2.0.3   htmltools_0.5.9