CN115166123A - Site specificity analysis method of abnormal N-glycolylneuraminic acid - Google Patents
Site specificity analysis method of abnormal N-glycolylneuraminic acid Download PDFInfo
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- CN115166123A CN115166123A CN202210820645.4A CN202210820645A CN115166123A CN 115166123 A CN115166123 A CN 115166123A CN 202210820645 A CN202210820645 A CN 202210820645A CN 115166123 A CN115166123 A CN 115166123A
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- G—PHYSICS
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- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
- G01N30/02—Column chromatography
- G01N30/88—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
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- G01N30/8651—Recording, data aquisition, archiving and storage
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- G—PHYSICS
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- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6848—Methods of protein analysis involving mass spectrometry
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
- G01N30/02—Column chromatography
- G01N30/88—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86
- G01N2030/8809—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample
- G01N2030/8813—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample biological materials
- G01N2030/8831—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample biological materials involving peptides or proteins
Abstract
The invention discloses a site specificity analysis method of abnormal N-glycolylneuraminic acid, which comprises the following steps: establishing a theoretical N-linked sugar database containing N-glycolylneuraminic acid monosaccharide based on an N-linked sugar pentasaccharide core structure, three N-linked sugar types and a biosynthesis rule; obtaining mass spectrum data of the glycopeptide to be detected, and screening the mass spectrum data based on the characteristic oxonium ions of the N-glycolyl neuraminic acid; carrying out qualitative and quantitative search on the screened spectrogram based on a theoretical N-linked sugar database; correlating the corresponding N-glycoprotein based on the identified polypeptide sequence of the intact N-glycopeptide comprising N-glycolyl neuraminic acid. The method can greatly improve the analysis speed and accuracy of the N-glycoprotein containing the NEU5Gc, and provides a foundation for related structure and function research.
Description
Technical Field
The invention belongs to the technical field of accurate analysis of protein structures, and particularly relates to a site specificity analysis method of abnormal N-glycolylneuraminic acid.
Background
Neu5Gc (aberrant N-glycolylneuraminic acid) is not normally present in humans due to the lack of a hydroxylase to convert CMP-Neu5Ac to CMP-Neu5 Gc; neu5Ac (N-acetylneuraminic acid) differs in structure from Neu5Gc (N-glyconeuraminic acid) by one oxygen atom (as shown in FIG. 1), and there is a difference between methyl and hydroxymethyl. However, neu5Gc has been observed in human cancer cells and tissues, and antibodies to Neu5Gc have been detected in healthy humans, which is a barrier to clinical xenotransplantation and stem cell therapy. Therefore, the research on Neu5Gc has important pathological and clinical significance.
The existing method adopts biochemical antibody to identify and detect Neu5Gc, has high analysis sensitivity, but can not give information of protein and sites. In view of the above problems, there is a need for further solutions.
Disclosure of Invention
In order to solve the above technical problems, the present invention aims to provide a method for site-specific analysis of abnormal N-glycolylneuraminic acid, which can greatly improve the speed and accuracy of analysis of N-glycoprotein containing NEU5Gc and provide a basis for relevant structural and functional studies.
In order to achieve the technical purpose and achieve the technical effect, the invention is realized by the following technical scheme:
a method for analyzing site specificity of abnormal N-glycolylneuraminic acid comprises the following steps:
1) Establishing a theoretical N-linked sugar database containing N-glycolylneuraminic acid monosaccharide based on an N-linked sugar pentasaccharide core structure, three N-linked sugar types and a biosynthesis rule;
2) Obtaining mass spectrum data of the glycopeptide to be detected, and screening the mass spectrum data based on the characteristic oxonium ions of the N-glycolyl neuraminic acid;
3) Carrying out qualitative and quantitative search on the screened spectrogram based on a theoretical N-linked sugar database;
4) Correlating the corresponding N-glycoprotein based on the identified polypeptide sequence of the intact N-glycopeptide comprising N-glycolyl neuraminic acid.
Further, the N-linked sugar pentasaccharide is N-acetylhexosamine, hexose, N-acetylneuraminic acid, N-glycolylneuraminic acid, and fucose, respectively.
Further, the three N-linked saccharide types are high mannose, complex and hybrid, respectively.
Further, in the step 3), the screened spectrogram is qualitatively and quantitatively searched by a GPSeekerPro search engine.
Further, the qualitative and quantitative search in step 3) is based on a target-decoy search and controls false positives not greater than 1%.
Further, the precursor ion and fragment ion mass spectra were allowed to deviate by 20ppm when performing qualitative and quantitative searches.
Further, in step 4), the corresponding N-glycoprotein is associated with the identified polypeptide sequence of the complete N-glycopeptide containing N-glycolyl neuraminic acid based on the protein database UniProt.
The beneficial effects of the invention are:
the method carries out qualitative and quantitative search on an N-glycopeptide liquid chromatography-mass spectrometry combined data set of a system to be detected based on a pre-constructed theoretical N-linked carbohydrate database containing NEU5Gc, and then associates corresponding N-glycoprotein based on the confirmed polypeptide sequence of the complete N-glycopeptide containing NEU5 Gc.
According to the invention, the NEU5Gc related tandem mass spectrum of the sample to be detected is screened based on the characteristic oxonium ion of the NEU5Gc in the tandem mass spectrum, so that the accuracy and the speed of identification are improved; the present invention is based on analysis at the level of intact N-glycopeptides, which is helpful for obtaining information on N-glycosylation sites; the invention is beneficial to quickly finding out the corresponding N-protein containing the NEU5Gc based on characteristic polypeptide sequence screening, and realizes the high-throughput and high-sensitivity identification of the N-glycoprotein containing the NEU5 Gc.
The method greatly improves the analysis speed and accuracy of the N-glycoprotein containing the NEU5Gc, and provides a basis for relevant structure and function research.
The method of the invention is applicable to the positioning analysis of any sugar chain modification site containing NEU5Gc, the qualitative and quantitative analysis of N-glycoprotein containing NEU5Gc, the searching tool which can carry out qualitative and quantitative searching on abnormal NEU5Gc related N-glycosylation at the level of N-linked sugar, N-glycopeptide and N-glycoprotein molecules, the analysis of abnormal NEU5Gc related N-glycoprotein at the level of N-linked sugar, N-glycopeptide and N-glycoprotein molecules, and the comprehensive analysis of protein information (such as amino acid change, other post-translational modification, artificial marker and the like) containing NEU5Gc glycosylation modification and other coexisting.
Drawings
FIG. 1 shows the chemical structures of Neu5Ac and Neu5 Gc.
FIG. 2 is a schematic flow chart of the analysis method of the present invention.
FIG. 3 shows the structural diagrams of three N-linked sugar types.
FIG. 4 is a secondary mass spectrum and a graphical dissociation of the complete N-glycopeptide comprising Neu5Gc identified on the N-glycosylation site N107 of the cell adhesion-4 (AC No. Q9UIA 0) No. 107, FIG. 4a is a secondary mass spectrum and FIG. 4b is a graphical dissociation graph.
Detailed Description
The technical solutions in the present invention will be described clearly and completely with reference to specific embodiments, and it should be understood that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
As shown in FIG. 2, the present invention provides a method for site-specific analysis of abnormal N-glycolylneuraminic acid, which comprises the following steps:
1) Establishing a theoretical N-linked sugar database containing N-glycolylneuraminic acid monosaccharide based on an N-linked sugar pentasaccharide core structure, three N-linked sugar types and a biosynthesis rule; wherein the N-linked sugar pentasaccharide is N-acetylhexosamine, hexose, N-acetylneuraminic acid, N-glycolylneuraminic acid and fucose respectively; the three N-linked sugar types are respectively a high mannose type, a complex type and a hybrid type;
2) Obtaining mass spectrum data of the glycopeptide to be detected, and screening the mass spectrum data based on the characteristic oxonium ions of the N-glycolyl neuraminic acid;
3) Based on a theoretical N-linked carbohydrate database, qualitatively and quantitatively searching the screened spectrogram through a GPSeekerPro search engine; the qualitative and quantitative search is based on a target-decoy search and controls false positives not greater than 1%; further, when qualitative and quantitative searching is carried out, the mass spectra of the precursor ions and the fragment ions are allowed to deviate by 20ppm;
4) The corresponding N-glycoprotein is associated based on the identified polypeptide sequence of the complete N-glycopeptide comprising N-glycolylneuraminic acid.
More specifically, in step 4), the corresponding N-glycoprotein is associated with the polypeptide sequence of the identified complete N-glycopeptide containing N-glycolyl neuraminic acid based on the protein database UniProt.
The present invention will be further illustrated below with reference to the site-specific analysis of abnormal N-glycolylneuraminic acid in human drug-resistant breast cancer cells.
Based on 3 types of N-linked sugars in human (including high mannose (Oligomannose), complex (Hybrid) and Hybrid (Complex) as shown in fig. 3), known rules of sugar chain biosynthesis and the equivalent transfer of sialyltransferase in sugar chain synthesis, a theoretical N-linked sugar database containing Neu5Gc was constructed, and some representative N-linked sugars are listed in table 1.
Table 1. Partial representative N-linked sugars containing N-glycolylneuraminic acid; y = N-acetylglucosamine, N-acetylglucosamine; m = manose, mannose; l = galactonase, galactose; f = Fu cose, fucose; v = N-acetylgalactosamine, N-acetylgalactosamine; s = N-acetylneuramic acid, N-acetylneuraminic acid; t = N-glycodeneuramicacid, N-glycolylneuraminic acid.
Obtaining the mass spectrum data of the N-glycopeptide of the human drug-resistant breast cancer cell, and screening the mass spectrum data based on the characteristic oxonium ion of the N-glycolylneuraminic acid. Wherein, the mass spectrum data of the N-glycopeptide of the human drug-resistant breast cancer cell is derived from an open N-glycopeptide LC-MS (Quantitative N-glycoproteomics study of cell-surface N-glycoproteomics markers of MCF-7/ADR cancer cells, analytical and biochemical, 2020,412, 2423-2432).
Based on Neu5Gc and Neu5Gc-H 2 O characteristic oxonium ions 308.09816 and 290.08759 (allowing for a 20ppm mass deviation) were filter screened for secondary mass spectra;
carrying out qualitative and quantitative database search on the screened secondary mass spectrogram by using an N-glycopeptide search engine GPSeekerPro based on the human body theory N-linked carbohydrate database containing Neu5Gc so as to confirm the polypeptide sequence of the complete N-glycopeptide containing N-glycolyl neuraminic acid; correlating the identified polypeptide sequences of the intact N-glycopeptides containing N-glycolylneuraminic acid to the corresponding N-glycoproteins based on the protein database Unit Prot (Unit Prot, www.uniprot.org). When qualitative and quantitative search is carried out, setting the mass spectrum allowable deviation of the precursor ions and the fragment ions to be 20ppm, and controlling false positive not to be more than 1% based on target-decoy search in a screened secondary mass spectrogram; out of 92 intact N-glycopeptides containing Neu5Gc identified from drug-resistant breast cancer MCF-7/ADR cells (Table 2); out of the drug-resistant breast cancer stem cells MCF-7/ADR CSCs, 101 intact N-glycopeptides containing Neu5Gc were identified (Table 3). The secondary mass spectrum and the graphical dissociation pattern of the intact N-glycopeptide GEGL NK-01Y (61F) 41Y41M (31M) 61M (21Y (31F) 41L 32T) 61Y comprising Neu5Gc identified from the N-glycosylation site N107 of the cytoadhesin-4 (AC No. Q9UI A0) No. 107 is shown in FIG. 4.
TABLE 2 intact N-glycopeptides containing Neu5Gc identified from drug-resistant breast cancer cells MCF-7/ADR, including the AC number of the intact N-glycoprotein in UniProt corresponding to intact N-glycopeptide, the N-glycosylation site corresponding to the amino acid sequence of intact N-glycoprotein, the amino acid sequence of the polypeptide backbone, the sugar chain structure of N-linked sugar, the intensity of the Neu5Gc oxonium ion in the secondary mass spectrum, the intensity of the oxonium ion after one molecule of water is lost by Neu5 Gc-H2O. Y = N-acetylglucosamine, N-acetylglucosamine; m = manose, mannose; l = galactose, galactose; f = Fucose, fucose; v = N-acetylgalactosamine, N-acetylgalactosamine; s = N-acetylneuraminic acid, N-acetylneuraminic acid; t = N-glycodeneuramicacid, N-glycolylneuraminic acid.
TABLE 3 intact N-glycopeptides containing Neu5Gc, identified from drug-resistant breast cancer stem cells MCF-7/ADR CSCs, including the AC number of the intact N-glycoprotein in Uniprot corresponding to intact N-glycopeptide, the N-glycosylation site corresponding to the amino acid sequence of intact N-glycoprotein, the amino acid sequence of the polypeptide backbone, the sugar chain structure of the N-linked sugar, the strength of Neu5Gc oxonium ion in the secondary mass spectrum, the loss of one water molecule of Neu5Gc (Neu 5 Gc-H) 2 Oxygen onium ion strength after O). Y = N-acetylglucosamine, N-acetylglucosamine; m = manose, mannose; l = galactose, galactose; f = F ucose, fucose; v = N-acetylgalactosamine, N-acetylgalactosamine; s = N-acetylneuramic acid, N-acetylneuraminic acid; t = N-glycodeneuramicacid, N-glycolylneuraminic acid.
The analysis method disclosed by the invention realizes targeted qualitative and quantitative search by using an N-glycopeptide search engine based on the established theoretical N-linked carbohydrate database containing Neu5Gc, and effectively improves the identification accuracy and efficiency of N-glycosylation of the protein related to the gene mutation by screening related N-glycoprotein containing Neu5Gc based on Neu5Gc characteristic oxonium ions in the secondary mass spectrum.
It is obvious to those skilled in the art that the present invention is not limited to the above embodiments, and it is within the scope of the present invention to adopt various insubstantial modifications of the method concept and technical scheme of the present invention, or to directly apply the concept and technical scheme of the present invention to other occasions without modification.
Claims (7)
1. A method for analyzing site specificity of abnormal N-glycolylneuraminic acid, which is characterized by comprising the following steps:
1) Establishing a theoretical N-linked sugar database containing N-glycolylneuraminic acid monosaccharide based on an N-linked sugar pentasaccharide core structure, three N-linked sugar types and a biosynthesis rule;
2) Obtaining mass spectrum data of the glycopeptide to be detected, and screening the mass spectrum data based on the characteristic oxonium ions of the N-glycolyl neuraminic acid;
3) Carrying out qualitative and quantitative search on the screened spectrogram based on a theoretical N-linked carbohydrate database;
4) The corresponding N-glycoprotein is associated based on the identified polypeptide sequence of the complete N-glycopeptide comprising N-glycolylneuraminic acid.
2. The method of claim 1, wherein the N-linked sugar pentasaccharide is N-acetylhexosamine, hexose, N-acetylneuraminic acid, N-glycolylneuraminic acid or fucose.
3. The method of claim 1, wherein the three N-linked sugar types are high mannose, complex and hybrid.
4. The method for analyzing the site specificity of abnormal N-glycolylneuraminic acid according to claim 1, wherein the step 3) is to perform qualitative and quantitative search on the screened spectrogram by a GPSeekerPro search engine.
5. The method for site-specific analysis of abnormal N-glycolylneuraminic acid according to claim 1, wherein the qualitative and quantitative search in step 3) is based on a target-decoy search, and false positives are controlled to be not more than 1%.
6. The method of claim 1, wherein the mass spectra of the precursor ion and the fragment ion are allowed to deviate by 20ppm when performing qualitative and quantitative search.
7. The method of claim 1, wherein in step 4), the identified N-glycoprotein is associated with the polypeptide sequence of the N-glycolylneuraminic acid-containing intact N-glycopeptide based on the protein database UniProt.
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