WO2023177035A1 - Procédé et instrument analytique pour l'analyse intégrée de glycopeptides à liaison n et à liaison o - Google Patents

Procédé et instrument analytique pour l'analyse intégrée de glycopeptides à liaison n et à liaison o Download PDF

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WO2023177035A1
WO2023177035A1 PCT/KR2022/015501 KR2022015501W WO2023177035A1 WO 2023177035 A1 WO2023177035 A1 WO 2023177035A1 KR 2022015501 W KR2022015501 W KR 2022015501W WO 2023177035 A1 WO2023177035 A1 WO 2023177035A1
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glycopeptide
score
glycopeptides
peak
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박건욱
이남용
김광회
이상용
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주식회사 셀키
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/62—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating the ionisation of gases, e.g. aerosols; by investigating electric discharges, e.g. emission of cathode
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • 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

Definitions

  • the technology described below relates to a technique for comprehensive quantitative analysis of N-linked and O-linked glycopeptides.
  • Glycosylation in which sugar chains are added to proteins, is divided into N-linked glycosylation and O-linked glycosylation.
  • Conventional programs for glycopeptide analysis cannot analyze N-linked glycopeptides and O-linked glycopeptides simultaneously.
  • conventional analysis techniques do not provide detailed analysis of modifications occurring in the sugar chain of glycopeptides.
  • the technology described below is intended to provide a technique for efficiently analyzing relatively low N-linked and O-linked glycopeptides simultaneously.
  • the integrated analysis method for N-linked and O-linked glycopeptides includes the steps of an analysis device receiving mass spectrum data for a sample, and the analysis device using tandem spectrum (MS/MS) data extracted from the mass spectrum data to determine the glycopeptide.
  • the N-linked and O-linked glycopeptide integrated analysis device selects the glycopeptide spectrum data using an input device that receives mass spectrum data for the sample and tandem spectrum (MS/MS) data extracted from the mass spectrum data,
  • MS/MS tandem spectrum
  • N-linked glycopeptides and O-linked glycopeptides are distinguished, and glycopeptides are modified based on peak values for certain candidate peaks for each of the N-linked glycopeptides or the O-linked glycopeptides.
  • glycoproteins which are disease-related biomarkers
  • the technology described below can effectively discover glycoproteins, which are disease-related biomarkers, by qualitatively and quantitatively analyzing glycopeptides of glycoproteins in human blood in their intact form.
  • glycosylation reaction N-/O-linked glycosylation, and glycosylation site, which are representative post-translational modifications added to the sugar chain of a protein, and can also identify N-/O-linked glycosylation and glycosylation sites.
  • N-/O-linked glycosylation and glycosylation sites which are representative post-translational modifications added to the sugar chain of a protein
  • N-/O-linked glycosylation and glycosylation sites can also identify N-/O-linked glycosylation and glycosylation sites.
  • -A variety of information can be provided, such as the type of linked sugar chain, increase in the number of side chains, and various modifications added to the sugar chain (O-Acetylation, Lactylation, Sulfation, Methylation, Mannose-6-Phosphate).
  • Figure 1 is an example of an N-linked and O-linked integrated glycopeptide analysis system.
  • Figure 2 is a schematic example of the process of N-linked and O-linked integrated glycopeptide analysis.
  • Figure 3 is an example of the process of obtaining sugar chain modification information during the analysis of N-linked and O-linked integrated glycopeptides.
  • Figure 4 is an example of 17 oxonium ions.
  • Figure 5 is an example of the result of calculating the sialic acid score.
  • Figure 6 is an example of peaks determining O-acetylation of sialic acid.
  • Figure 7 is an example of peaks that determine lactic acid oxidation of sialic acid.
  • Figure 8 is an example of peaks that determine sulfation of sialic acid.
  • Figure 9 is an example of peaks determining lactation of GlcNAc.
  • Figure 10 is an example of peaks determining phosphorylation of mannose.
  • Figure 11 is an example of an analysis device for integrated analysis of N-linked and O-linked glycopeptides.
  • first, second, A, B, etc. may be used to describe various components, but the components are not limited by the terms, and are only used for the purpose of distinguishing one component from other components. It is used only as For example, a first component may be named a second component without departing from the scope of the technology described below, and similarly, the second component may also be named a first component.
  • the term and/or includes any of a plurality of related stated items or a combination of a plurality of related stated items.
  • each component is responsible for. That is, two or more components, which will be described below, may be combined into one component, or one component may be divided into two or more components for more detailed functions.
  • each of the components described below may additionally perform some or all of the functions handled by other components, and some of the main functions handled by each component may be performed by other components. Of course, it can also be carried out exclusively by .
  • each process forming the method may occur in a different order from the specified order unless a specific order is clearly stated in the context. That is, each process may occur in the same order as specified, may be performed substantially simultaneously, or may be performed in the opposite order.
  • the technique described below is a technique for analyzing N-linked glycopeptides and O-linked glycopeptides in samples.
  • sample is generally blood (serum) from which glycopeptides are to be analyzed.
  • sample may be another type of sample that can be analyzed for glycopeptides.
  • object of analysis basically refers to humans.
  • analysis target may be animals, plants, insects, yeast, etc.
  • Hydrolysis refers to the process of separating sugars from glycoproteins.
  • the hydrolysis may be performed using any method well known in the art.
  • the hydrolysis can be performed using hydrolytic enzymes, specifically trypsin, arginine C (Arg-C), aspartic acid N (Asp-N), and glutamic acid C (Glu-C).
  • hydrolytic enzymes specifically trypsin, arginine C (Arg-C), aspartic acid N (Asp-N), and glutamic acid C (Glu-C).
  • Arg-C arginine C
  • Asp-N aspartic acid N
  • Glu-C glutamic acid C
  • tandem spectrum refers to a spectrum analyzed by selecting ions of interest or ions with relatively high sensitivity from the entire mass spectrum (MS).
  • the tandem spectrum may be a collision-induced dissociation (CID) or higher-energy C-trap dissociation (HCD)-MS/MS spectrum.
  • the analysis device analyzes the spectral data to analyze N-linked glycopeptides and O-linked glycopeptides.
  • the analysis device can be implemented as a variety of devices capable of processing certain data.
  • an analysis device can be implemented as a PC, a server on a network, a smart device, or a chipset with a dedicated program embedded therein.
  • Figure 1 is an example of an analysis system 100 through N-linked and O-linked glycopeptides.
  • Integrated analysis of N-linked and O-linked glycopeptides refers to analyzing both N-linked glycopeptides and O-linked glycopeptides through one analysis process.
  • the analysis device is a computer terminal 130 and/or a server 140.
  • the high-resolution mass spectrometer 110 performs mass analysis on the sample.
  • the high-resolution mass spectrometer 110 generates mass spectrum data in the form of digital data as a mass analysis result.
  • the high-resolution mass spectrometer 110 may store the generated mass spectrum data in a separate database (DB, 120).
  • the user (A) can analyze spectral data using the computer terminal 130 and perform integrated analysis of N-linked and O-linked glycopeptides.
  • the computer terminal 130 may receive spectrum data from the high-resolution mass spectrometer 110 or DB 120 through a wired or wireless network. In some cases, the computer terminal 130 may be a device physically connected to the high-resolution mass spectrometer 110.
  • the computer terminal 130 calculates the results of integrated analysis of N-linked and O-linked glycopeptides based on the initial mass spectrum data.
  • the computer terminal 130 can calculate the signal to noise ratio (SNR) from each spectrum data, and use it for analysis if the SNR value is less than a certain value (for example, 2).
  • SNR signal to noise ratio
  • Server 140 may receive spectral data from high-resolution mass spectrometer 110 or DB 120.
  • the server 140 can calculate the SNR from each spectrum data and use it for analysis only when the SNR value is less than or equal to a certain value (eg, 2).
  • the server 140 calculates the results of integrated analysis of N-linked and O-linked glycopeptides based on the initial mass spectrum data. The specific N-linked and O-linked glycopeptide integrated analysis process will be described later.
  • the server 140 may transmit the analysis results to user A's terminal. User A can check the analysis results for the sample.
  • Figure 2 is an example of a schematic process 200 of integrated analysis of N-linked and O-linked glycopeptides.
  • the analysis device receives initial mass spectral data.
  • Initial mass spectral data refers to data generated by a mass spectrometer analyzing a sample.
  • the analysis device can extract MS (mass spectrum) data and tandem spectrum (MS/MS) data from the initial mass spectrum data (210).
  • MS mass spectrum
  • MS/MS tandem spectrum
  • the analysis device can extract ms1 (MS) and ms2 (MS/MS) files from the initial mass spectral data using RAWConverter v1.1 (The Scripps Research Institute, USA).
  • the analysis device selects the spectrum of the glycopeptide using MS/MS data (200).
  • the analysis device can select only the spectrum of glycopeptides by setting a value to distinguish between peptides and glycopeptides in the sample.
  • the analysis device can check the peaks and intensity of the peaks identified in each tandem spectrum and determine a value for distinguishing peptides from glycopeptides based on the distribution of certain scores calculated using this.
  • the analysis device can distinguish N-linked glycopeptides and O-linked glycopeptides based on the score used to distinguish the glycopeptide spectrum (230).
  • the analysis device can obtain isotope distribution based on MS data and identify N-linked glycopeptides and O-linked glycopeptides by comparing it with a previously constructed database (240).
  • the analysis device can perform quantitative analysis on N-linked glycopeptides and O-linked glycopeptides, respectively (250).
  • Quantitative analysis may include information on the amount of the corresponding glycopeptide, type of sugar chain, modifications added to the sugar chain, etc.
  • Figure 3 is an example of the process (300) of obtaining sugar chain modification information during the integrated analysis process of N-linked and O-linked glycopeptides.
  • Figure 3 is an example of the process of performing quantitative analysis by distinguishing N-linked glycopeptides and O-linked glycopeptides from initial mass spectrum data using MS/MS data.
  • Figure 3 explains in particular the process of confirming the modification of the sugar chain.
  • the analysis device first extracts MS/MS data from the initial mass spectrum data.
  • the analysis device can calculate the following MM-score based on certain candidate peaks in MS/MS data (310).
  • the analysis device calculates the MM score from each tandem spectrum using a peak group (Oxonium ion peaks) consisting of a total of 17 peaks.
  • a peak group (Oxonium ion peaks) consisting of a total of 17 peaks.
  • Table 1 below is an example of peak groups. Each peak group is defined by its mass-to-charge ratio (m/z).
  • the analysis device calculates the MM score expressed in Equation 1 below from each tandem spectrum of the peak group.
  • N is the total number of oxonium ions. That is, N may be 17.
  • I i is the intensity of the observed ith peak, and I max is the base peak intensity (BPI).
  • C is a constant value.
  • MassError refers to the difference between experimental and theoretical values. The theoretical value refers to the theoretical peak intensity for the corresponding ion.
  • the analysis device can select only the glycopeptide spectrum by applying Gaussian fitting to the MM score distribution for the peaks.
  • the analysis device can distinguish the N-linked glycopeptide spectrum and the O-linked glycopeptide spectrum from the glycopeptide spectrum selected using the MM score distribution (320).
  • the analysis device can distinguish between the N-linked glycopeptide spectrum and the O-linked glycopeptide spectrum based on the value of the peak of a specific band based on O i used in Equation 1.
  • the analysis device can distinguish between the N-linked glycopeptide spectrum and the O-linked glycopeptide spectrum based on the value (GGRatio) calculated through Equation 2 below.
  • Equation 2 the value in parentheses refers to a specific mass-to-charge ratio (m/z). If GGRatio ⁇ 3, the analysis device determines that the spectrum is an O-linked glycopeptide spectrum. If GGRatio ⁇ 3, the analysis device determines that the spectrum is an N-linked glycopeptide spectrum.
  • the analysis device can perform quantitative analysis on N-linked glycopeptides and O-linked glycopeptides, respectively.
  • Figure 3 shows the process of calculating additional sugar chain modification information for N-linked glycopeptides.
  • sugar chain modification information can also be calculated through a similar process.
  • Figure 4 is an example of 17 oxonium ions. It corresponds to the peak group that serves as the standard for calculating the MM score described in Figure 3 and Table 1. Modifications that can occur in glycans include O-Acetylation (42.01002, NeuAc or NeuGc), Lactylation (71.01276, NeuAc or NeuGc or GalNAc), and Sulfation ( 79.95627, NeuAc or NeuGc).
  • the analysis device first distinguishes between glycopeptides with sialic acid and glycopeptides without sialic acid based on the sialic acid score (SiA-score) (330).
  • SiA-score sialic acid score
  • the SiA- score can be expressed as Equation 3 below.
  • SiA- score corresponds to the sum of the intensities of the peaks for all sialic acids (NeuAc and/or NeuGc).
  • Sialic acid i refers to the peak intensity of the ith sialic acid.
  • the analysis device can distinguish glycopeptides based on the SiA- score as shown in Table 2 below.
  • the analysis device determines that the glycopeptide contains sialic acid if the SiA- score is ⁇ 15.
  • the analysis device can judge a glycopeptide without sialic acid if the SiA- score is ⁇ 15.
  • Figure 5 is an example of the result of calculating the sialic acid score.
  • Figure 5(A) is an example showing the peak that serves as the standard for calculating the sialic acid score.
  • the sialic acid score calculates the score for all of the various types (sialic acid-related ions among the 17 oxonium ions) that can appear in NeuAc and NeuGc.
  • Figure 5(B) is an example showing the results corresponding to the cases (Case 1 to Case 4) in Table 2 above. The vertical axis in Figure 5(B) represents relative abundance.
  • the analysis device confirms possible sugar chain modifications for each glycopeptide without sialic acid or glycopeptide with sialic acid. For this purpose, the analysis device calculates a modification score (Mod-score) for each modification (340 or 350). The analysis device calculates a Mod-score for each possible transformation, and if the Mod-score is greater than a threshold, it can be judged to be a specific variant. For example, if the Mod-score of a specific variant is 10 or more, the analysis device can determine it to be the corresponding variant (yes of 340 or yes of 350). The analysis device can judge the glycopeptide as unmodified if the Mod-score for all modifications is less than 10 (no of 340 or no of 350). Below is a description of each Mod-score.
  • Mod-score modification score
  • Figure 6 is an example of peaks determining O-acetylation of sialic acid.
  • the analysis device can determine 0-acetylation of sialic acid based on the Mod-score expressed in Equation 4 and Equation 5 below.
  • Equation 4 is the equation for mono-acetylation
  • Equation 5 is the equation for di-acetylation.
  • the analysis device may determine that mono-acetylation of sialic acid exists if the Mod-score of Equation 4 is greater than or equal to a threshold value (e.g., 10).
  • a threshold value e.g. 10
  • N is the total number of expected specific ions (total number of peaks in FIG. 6)
  • n is the number of ions confirmed in the sample
  • I mi is the intensity of the observed ith peak
  • I max is the basal peak intensity (BPI).
  • Figure 7 is an example of peaks that determine lactic acid oxidation of sialic acid.
  • the analysis device can determine lactation of sialic acid based on the Mod-score expressed in Equation 6 below. For example, the analysis device can determine that sialic acid is acidified if the Mod-score of Equation 6 is greater than or equal to a threshold value (e.g., 10).
  • a threshold value e.g. 10
  • N is the total number of expected specific ions (total number of peaks in Figure 7)
  • n is the number of ions identified in the sample
  • I mi is the intensity of the observed ith peak
  • I max is the basis Peak intensity (BPI).
  • Figure 8 is an example of peaks that determine sulfation of sialic acid.
  • the analysis device can determine the lactic acid oxidation of sialic acid based on the Mod-score expressed in Equation 7 below. For example, the analysis device may determine that there is sulfation of sialic acid if the Mod-score of Equation 7 is greater than or equal to a threshold value (e.g., 10).
  • a threshold value e.g. 10
  • N is the total number of expected specific ions (total number of peaks in Figure 8)
  • n is the number of ions identified in the sample
  • I mi is the intensity of the observed ith peak
  • I max is the basis Peak intensity (BPI).
  • Figure 9 is an example of peaks determining lactation of GlcNAc (N-Acetylglucosamine).
  • the analysis device can determine lactation of GlcNAc based on the Mod-score expressed in Equation 8 below. For example, the analysis device can determine that there is sulfation of GlcNAc if the Mod-score of Equation 8 is greater than or equal to a threshold value (eg, 10).
  • a threshold value eg, 10
  • N is the total number of expected specific ions (total number of peaks in Figure 9)
  • n is the number of ions identified in the sample
  • I mi is the intensity of the observed ith peak
  • I max is the basis Peak intensity (BPI).
  • Figure 10 is an example of peaks that determine phosphorylation of mannose.
  • the analysis device can determine the phosphorylation of mannose based on the Mod-score expressed in Equation 9 below. For example, the analysis device may determine that there is phosphorylation of mannose if the Mod-score of Equation 9 is greater than or equal to a threshold value (eg, 10).
  • a threshold value eg, 10
  • N is the total number of expected specific ions (total number of peaks in Figure 10)
  • n is the number of ions identified in the sample
  • I mi is the intensity of the observed ith peak
  • I max is the basis Peak intensity (BPI).
  • the analysis device can classify the modification of the sugar chain using the sialic acid score (SiA-score) and modification score (Mod-score) as shown in Table 3 below.
  • Figure 11 is an example of an analysis device for integrated analysis of N-linked and O-linked glycopeptides.
  • the analysis device 400 corresponds to the above-described analysis devices (130 and 140 in FIG. 1).
  • the analysis device 400 may be physically implemented in various forms.
  • the analysis device 400 may take the form of a computer device such as a PC, a network server, or a chipset dedicated to data processing.
  • the analysis device 400 may include a storage device 410, a memory 420, an arithmetic device 430, an interface device 440, a communication device 450, and an output device 460.
  • the storage device 410 may store a program for analyzing N-linked glycopeptides and O-linked glycopeptides in the initial mass spectrum data.
  • the storage device 410 can store isotope peaks and relative intensity values of the peaks, which are theoretical examples for identifying glycopeptides.
  • the storage device 410 may store the analysis results.
  • the memory 420 may store data and information generated while the analysis device 400 analyzes mass spectrum data.
  • the interface device 440 is a device that receives certain commands and data from the outside.
  • the interface device 440 may receive initial spectrum data from a physically connected input device or an external storage device.
  • the interface device 440 may also receive separate experimental data input from the user.
  • the interface device 440 may transmit the analysis result to an external object.
  • the communication device 450 refers to a configuration that receives and transmits certain information through a wired or wireless network.
  • the communication device 450 may receive initial spectrum data from an external object.
  • the communication device 450 may also receive separate experimental data required for analysis.
  • the communication device 450 may transmit the analysis results to an external object such as a user terminal.
  • the interface device 440 and the communication device 450 are components that exchange certain data with a user or other physical object, they can also be collectively referred to as input/output devices. If limited to information or data input functions, the interface device 440 and communication device 450 may be referred to as input devices.
  • the output device 460 is a device that outputs certain information.
  • the output device 460 can output the interface required for the data processing process, analysis results, and visual data about the analysis content.
  • the computing device 430 may extract MS data and/or MS/MS data from the initial mass spectrum data.
  • the calculation device 430 can calculate the MM score from MS/MS data.
  • the computing device 430 may select the glycopeptide spectrum by performing Gaussian fitting on the distribution of MM scores.
  • the calculation device 430 can calculate the above-described GGRatio to distinguish between N-linked glycopeptides and O-linked glycopeptides.
  • the computing device 430 can perform necessary quantitative analysis on the classified N-linked glycopeptides and O-linked glycopeptides, respectively.
  • the calculation device 430 can confirm and quantify the modification of sugar chains.
  • the calculation device 430 can calculate the above-described SiA-score and distinguish between glycopeptides with sialic acid and glycopeptides without sialic acid based on the SiA-score.
  • the calculation device 430 calculates the above-described Mod-score for each glycopeptide with sialic acid or glycopeptide without sialic acid to confirm the type of sugar chain modification and quantify the modification.
  • the calculation unit 430 calculates the Mod-score for each modification, and if the score is above a certain threshold, it can be determined that the corresponding glycopeptide has the corresponding sugar chain modification. This process is the same as described in Equations 4 to 9.
  • the computing device 430 may be a device such as a processor that processes data and performs certain operations, an AP, or a chip with an embedded program.
  • sample analysis method, glycopeptide analysis method, and integrated N-linked and O-linked glycopeptide analysis method as described above may be implemented as a program (or application) including an executable algorithm that can be executed on a computer.
  • the program may be stored and provided in a temporary or non-transitory computer readable medium.
  • a non-transitory readable medium refers to a medium that stores data semi-permanently and can be read by a device, rather than a medium that stores data for a short period of time, such as registers, caches, and memories.
  • the various applications or programs described above include CD, DVD, hard disk, Blu-ray disk, USB, memory card, ROM (read-only memory), PROM (programmable read only memory), and EPROM (Erasable PROM, EPROM).
  • EEPROM Electrically EPROM
  • Temporarily readable media include Static RAM (SRAM), Dynamic RAM (DRAM), Synchronous DRAM (SDRAM), Double Data Rate SDRAM (DDR SDRAM), and Enhanced SDRAM (Enhanced RAM). It refers to various types of RAM, such as SDRAM (ESDRAM), Synchronous DRAM (Synclink DRAM, SLDRAM), and Direct Rambus RAM (DRRAM).
  • SRAM Static RAM
  • DRAM Dynamic RAM
  • SDRAM Synchronous DRAM
  • DDR SDRAM Double Data Rate SDRAM
  • Enhanced SDRAM Enhanced SDRAM
  • ESDRAM Synchronous DRAM
  • SLDRAM Synchronous DRAM
  • DRRAM Direct Rambus RAM

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Abstract

Ce procédé d'analyse intégrée de glycopeptides à liaison N et à liaison O comprend les étapes dans lesquelles un instrument analytique : reçoit des données de spectre de masse d'un échantillon ; sélectionne uniquement les données de spectre de glycopeptide à l'aide des données de spectre en tandem (MS/MS) extraites des données de spectre de masse ; identifie un glycopeptide à liaison N et un glycopeptide à liaison O à partir des données de spectre de glycopeptides ; et détermine une modification de la chaîne de sucres sur la base des valeurs de pic de pics candidats prédéterminés pour chacun du glycopeptide à liaison N ou du glycopeptide à liaison O.
PCT/KR2022/015501 2022-03-15 2022-10-13 Procédé et instrument analytique pour l'analyse intégrée de glycopeptides à liaison n et à liaison o WO2023177035A1 (fr)

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