sugarMassesPredict

command line tool to calculate all possible glycan molecules and the m/z values of their ions given a set of input parameters

NOTE: I have now also added an 'R' version - if you use the reticulate package in R, you can source the file (sugarMassesPredict-r.py) and then use the function 'predict_sugars' directly in R to generate output there.

this tool is being frequently updated :) if you have any questions or issue please feel free to contact me at mbligh@mpi-bremen.de

word of caution: please note that this tool will predict sugars that are not possible as the nature of sugar chemistry means that it would take a long time to add in all the constraints!

e.g.

library(reticulate)
py_install("pandas", "numpy")
source_python("sugarMassesPredict-r.py")
dp1 = as.integer(1)
dp2 = as.integer(3)
ESI_mode = 'pos'
scan_range1 = as.integer(100)
scan_range2 = as.integer(800)
pent_option = as.integer(1)
modifications = list('sulphate', 'deoxy')
label = "procainamide"
df <- predict_sugars(dp1 = dp1, dp2 = dp2, ESI_mode = ESI_mode, scan_range1 = scan_range1, scan_range2 = scan_range2, pent_option = pent_option, modifications = modifications, label = label)

dependencies

pandas
numpy
python 3

input parameters

required

dp (degree of polymerisation) range
whether pentose monomers should be used in addition to hexose
modifications - possible options are none, all, or any combination of:
- sulphate
- carboxyl
- phosphate
- deoxy
- N-acetyl
- O-acetyl
- O-methyl
- anhydrobridge
- unsaturated
- alditol
- amino
- dehydrated
maximum number of modifications per monomer on average
ionisation mode
scan range (m/z)

optional

label - current options are procainamide (added by reductive amination) and benzoic acid (added on free alcohol groups, will calculate glycans with no label to the maximum number of labels possible)
output file path - defaults to "predicted_sugars.txt"
options to do with the calculation of the possible number of structural isomers (but this section needs to be fixed)

output

tab delimited text file with one row per molecule. m/z values outside the scan range as shown as "NA", and molecules with no ions with m/z values within the scan are not returned. columns are as follows:

degree of polymerisation (dp)
name
monoisotopic mass (Da)
sum formula
columns with m/ values of possible ions given the input parameters.
- positive mode:
  - [M+H]⁺
  - [M+Na]⁺
- negative mode:
  - [M+Cl]^-
  - [M+CHOO]^-
  - [M+2Cl]^2-
  - [M+2CHOO]^2-
  - [M+Cl-H]^2-
  - [M+CHOO-H]^2-
  - [M+CHOO+Cl]^2-
  - [M-nH]^n-, where n is 1 to the maximum number anionic groups that any single molecule in the table has
if parameters related to isomers were specified in the input, there is an additional column for the number of possible isomers per molecule

how to run

the help menu accessed with:

sugarMassesPredict.py -h

returns the following:

usage: sugarMassesPredict.py [-h] -dp int int [-p int] -m str [str ...]
                             [-n int] [-ds int] [-ld str [str ...]] [-oh int]
                             [-b int] -i str [str ...] -s int int [-l label]
                             [-o filepath]

Script to predict possible masses of unknown sugars. Written by Margot Bligh.

optional arguments:
  -h, --help            show this help message and exit
  -dp int int, --dp_range int int
                        DP range to predict within: two space separated
                        numbers required (lower first)
  -p int, --pent_option int
                        should pentose monomers be considered as well as
                        hexose: 0 for no {default}, 1 for yes
  -m str [str ...], --modifications str [str ...]
                        space separated list of modifications to consider.
                        note that alditol and unsaturated are max once per
                        saccharide. allowed values: none OR all OR any
                        combination of carboxyl, phosphate, deoxy, nacetyl,
                        omethyl, anhydrobridge, oacetyl, unsaturated, alditol,
                        sulphate
  -n int, --nmod_max int
                        max no. of modifications per monomer on average
                        {default 1}. does not take into account unsaturated or
                        alditol.
  -ds int, --double_sulphate int
                        can monomers be double-sulphated: 0 for no {default},
                        1 for yes. for this you MUST give a value of at least
                        2 to -n/--nmod_max
  -ld str [str ...], --LorD_isomers str [str ...]
                        isomers calculated for L and/or D enantiomers {default
                        D only}. write space separated if both
  -oh int, --OH_stereo int
                        stereochem of OH groups considered when calculating
                        no. of isomers: 0 for no {default}, 1 for yes
  -b int, --bond_stereo int
                        stereochem of glycosidic bonds and reducing end
                        anomeric carbons considered when calculating no. of
                        isomers: 0 for no {default}, 1 for yes
  -i str [str ...], --ESI_mode str [str ...]
                        neg and/or pos mode for ionisation (space separated if
                        both)
  -s int int, --scan_range int int
                        mass spec scan range to predict within: two space
                        separated numbers required (lower first)
  -l label, --label label
                        name a label added to the oligosaccharide. if not
                        labelled do not include. options: procainamide OR
                        benzoic_acid.
  -o filepath, --output filepath
                        filepath to .txt file for output table {default:
                        predicted_sugars.txt}