A glycan structure analyzer configured to analyze a structure of a sialic-acid-linked glycan based on mass spectrum data obtained by a mass spectrometric analysis of a sample containing the sialic-acid-linked glycan or a molecule modified with the glycan which have been pretreated with a chemical modification agent specific to the sialic-acid linkage type which causes different mass change depending on the sialic-acid linkage type, the glycan structure analyzer comprising: a condition setting section configured to allow a user to set an ion species to be analyzed, a polarity of an electric charge of the ion species, and mass change factors each of which causes a mass change of a glycan through a modification; a glycan core structure information acquisition section configured to acquire various glycans having a core structure formed by a plurality of monosaccharide residues of a plurality of kinds, wherein the glycans are in their respective original forms which have not undergone any modification, and are not ionized yet, and mass information corresponding to each of those glycans; a theoretical mass calculation section configured to calculate a theoretical glycan mass-to-charge ratio for each of the various glycans acquired by the glycan core structure information acquisition section, by increasing or decreasing a mass of the glycan based on the mass change factors set through the condition setting section, wherein different values of mass change are added to or subtracted from the mass of the glycan based on the mass change factors set through the condition setting section; and a glycan structure estimation section configured to estimate a structure of a glycan by comparing the theoretical glycan mass-to-charge ratio of the glycan with a mass-to-charge ratio of an ion peak in given mass spectrum data, wherein: the condition setting section includes a mass change setting section for sialic-acid-linkage-specific chemical modification, configured to allow the user to set, as one of the mass change factors, a chemical modification specific to a linkage type of a sialic acid separately from other kinds of modifications which causes different mass change depending on the sialic-acid linkage type; and the theoretical mass calculation section is configured to determine the theoretical glycan mass-to-charge ratio by increasing or decreasing the mass for each sialic-acid linkage type according to the chemical modification set through the mass change setting section for sialic-acid-linkage-specific chemical modification, wherein different values of mass change are added to or subtracted from the mass for each sialic-acid linkage type according to the chemical modification set through the mass change setting section for sialic-acid-linkage-specific chemical modification. a condition setting section configured to allow a user to set an ion species to be analyzed, a polarity of an electric charge of the ion species, and mass change factors each of which causes a mass change of a glycan through a modification; a glycan core structure information acquisition section configured to acquire various glycans having a core structure formed by a plurality of monosaccharide residues of a plurality of kinds, wherein the glycans are in their respective original forms which have not undergone any modification, and are not ionized yet, and mass information corresponding to each of those glycans; a theoretical mass calculation section configured to calculate a theoretical glycan mass-to-charge ratio for each of the various glycans acquired by the glycan core structure information acquisition section, by increasing or decreasing a mass of the glycan based on the mass change factors set through the condition setting section, wherein different values of mass change are added to or subtracted from the mass of the glycan based on the mass change factors set through the condition setting section; and a glycan structure estimation section configured to estimate a structure of a glycan by comparing the theoretical glycan mass-to-charge ratio of the glycan with a mass-to-charge ratio of an ion peak in given mass spectrum data, the condition setting section includes a mass change setting section for sialic-acid-linkage-specific chemical modification, configured to allow the user to set, as one of the mass change factors, a chemical modification specific to a linkage type of a sialic acid separately from other kinds of modifications which causes different mass change depending on the sialic-acid linkage type; and the theoretical mass calculation section is configured to determine the theoretical glycan mass-to-charge ratio by increasing or decreasing the mass for each sialic-acid linkage type according to the chemical modification set through the mass change setting section for sialic-acid-linkage-specific chemical modification, wherein different values of mass change are added to or subtracted from the mass for each sialic-acid linkage type according to the chemical modification set through the mass change setting section for sialic-acid-linkage-specific chemical modification.