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Automatic annotation of matrix‐assisted laser desorption/ionization N ‐glycan spectra
Author(s) -
Goldberg David,
SuttonSmith Mark,
Paulson James,
Dell Anne
Publication year - 2005
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200401071
Subject(s) - annotation , glycan , computer science , mass spectrometry , mass spectrum , matrix (chemical analysis) , binary number , chemistry , computational biology , artificial intelligence , chromatography , biology , mathematics , biochemistry , arithmetic , glycoprotein
Matrix‐assisted laser desorption/ionization‐mass spectrometry (MALDI‐MS) is the pre‐eminent technique for mass mapping of glycans. In order to make this technique practical for high‐throughput screening, reliable automatic methods of annotating peaks must be devised. We describe an algorithm called Cartoonist that labels peaks in MALDI spectra of permethylated N ‐glycans with cartoons which represent the most plausible glycans consistent with the peak masses and the types of glycans being analyzed. There are three main parts to Cartoonist. (i) It selects annotations from a library of biosynthetically plausible cartoons. The library we currently use has about 2800 cartoons, but was constructed using only about 300 archetype cartoons entered by hand. (ii) It determines the precision and calibration of the machine used to generate the spectrum. It does this automatically based on the spectrum itself. (iii) It assigns a confidence score to each annotation. In particular, rather than making a binary yes/no decision when annotating a peak, it makes all plausible annotations and associates them with scores indicating the probability that they are correct.