CN108445221B - Identification method of protein methylation - Google Patents

Identification method of protein methylation Download PDF

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CN108445221B
CN108445221B CN201710083220.9A CN201710083220A CN108445221B CN 108445221 B CN108445221 B CN 108445221B CN 201710083220 A CN201710083220 A CN 201710083220A CN 108445221 B CN108445221 B CN 108445221B
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spectrogram
methionine
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methylation
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叶明亮
王科云
毛家维
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Dalian Institute of Chemical Physics of CAS
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Abstract

The invention relates to a novel method for identifying protein methylation, which utilizes novel re-labeled methionine to mark methylation sites, develops a methylated peptide fragment analysis method which integrates methionine cell culture amino acid stable isotope labeling, identifies and extracts a fragmentation spectrogram of a methylated peptide fragment and spectral peak demethylation treatment, and applies the methylated peptide fragment analysis method to the large-scale analysis of methylated proteome. The amino acid labeling mode introduced in the invention can distinguish methylated peptide fragments from peptide fragments containing methionine, and obtains the spectrogram of non-methylated peptide fragments by identifying and extracting fragmentation spectrogram from methylated peptide fragments and carrying out demethylation treatment on the fragmentation spectrogram. And determining the sequence of the peptide fragment through database search, and determining the modification site by combining a spectrogram of the methylated modified peptide fragment. This method does not require the type of modification to be preset and thus allows simultaneous analysis of all known types of methylation.

Description

Identification method of protein methylation
Technical Field
The invention belongs to the technical field of proteomics research direction methylated proteomics, and particularly relates to a novel method for identifying a methylated proteome.
Background
Methylation modification of proteins is catalyzed by S-adenosylmethionine (SAM) -dependent methyltransferases and is one of the most common post-translational modifications of proteins. Methylation modification plays an important regulatory role in the regulation of a wide variety of physiological processes. The research shows that: protein methylation may modulate intra-or intermolecular interactions of a protein of interest; affect their affinity for RNA and thus affect a variety of cellular processes including transcriptional regulation, cellular localization, ribosome assembly, RNA processing, maturation of heterogeneous ribonucleic acid ribosomal proteins (hnRNPs), protein-protein interactions, translational accuracy, nuclear trafficking, protein nucleic acid trafficking and metabolism, and intracellular signaling. Due to the diversity and complexity of methylation modifications, identifying methylation sites remains very difficult at the proteomic level, mainly because methylation modifications of proteins can occur at up to 8 amino acid residues, including 11 methylated forms. The traditional post-translational modification processing strategy is to set the type of post-translational modification to be studied as a variable modification. Therefore, when the methylation modification sites are identified, if the methylation modification types are set as variable modifications, a large number of variable modifications are required to be simultaneously set, the library searching space is quite large, and the false positive rate is also high.
Methionine is an essential amino acid that mammalian cells cannot synthesize by themselves, and is also a precursor for the synthesis of S-adenosylmethionine. If the heavy-isotope labeled methionine is added at the time of cell culture, the heavy-isotope labeled methyl group is transferred to the side chain of the target amino acid with the aid of methyltransferase. If methionine composed of different isotopes is used to mark a methylation site on a protein, there is a fixed difference in the molecular weight of the parent ion between the light and heavy forms of the same methylated peptide, and this difference in molecular weight is determined by the number of methyl modifications on the peptide, so that the number of methylation modifications on the peptide can be determined by this difference in molecular weight. However, in the conventional labeling method (document 1: S. -E.Ong, G.Mittler, M.Mann, identification and quantification in vivo methylation sites by molecular weight SILAC, Nat Methods 1(2004)119-126), the difference in molecular weight introduced by isotopic labeling is the same for the peptide fragment containing methionine and the peptide fragment containing methylation modification, and thus the two types of peptide fragments cannot be distinguished. The invention utilizes an analysis method which integrates methionine cell culture amino acid stable isotope labeling, identifies fragmentation spectrogram and spectral peak demethylation of methylated peptide segments for the first time, and applies the analysis method to the scale analysis of methylated proteome. By identifying and extracting the fragmentation spectrum peak of the methylated peptide segment and carrying out demethylation treatment on the fragmentation spectrum peak, the spectrum peak of the unmethylated peptide segment is further obtained, and the database searching process is greatly simplified. And the modification sites can be positioned by combining the spectrogram of the methylation modified peptide fragment. This method does not require a preset type of modification and thus allows simultaneous analysis of multiple methylation modifications.
Disclosure of Invention
The invention aims to provide a high-throughput novel methylated protein component analysis method which integrates the methionine cell culture amino acid stable isotope labeling technology, the identification of the fragmentation spectrogram of a methylated peptide fragment and the spectral peak demethylation.
The novel method for analyzing the methylated proteome sample provided by the invention utilizes the characteristic that the molecular weight difference between the light-scale methylated peptide fragment and the heavy-scale methylated peptide fragment is directly related to the number of the methylated groups, and realizes the identification based on the methylated peptide fragment spectrogram and the peak demethylation treatment.
The method comprises the following specific steps:
(1) culturing the cells in DMEM culture solution containing light-mark methionine and heavy-mark methionine;
(2) carrying out ultrasonic-assisted disruption on the cells obtained in the step (1) in a lysis solution, and mixing according to the proportion of 1:1 of the protein amount;
(3) carrying out enzyme digestion treatment on the protein sample obtained in the step (2);
(4) and (4) carrying out high-resolution mass spectrometry on the protease hydrolysate obtained in the step (3).
(5) And (4) identifying the fragmentation spectrogram of the methylated peptide fragment in the mass spectrum data obtained in the step (4), performing spectral peak demethylation treatment, and further performing database search to determine the peptide fragment sequence.
(6) Combining the peptide fragment sequence obtained in the step (5) and a spectrogram before demethylation to determine a methylation modification site;
the cells used in the present invention are selected from human cells, such as HEK293 cells, HepG2 cells, HeLa cells or Jurkat cells.
The cell culture system described in step (1) contains 0.2mM of L-methionine or L-methionine-carboxyl-13C, methyl-D3DMEM medium, and 10% dialyzed fetal bovine serum was added.
The cell lysis system described in step (2) is a buffer solution containing 6-8M urea, 1-2% v/v polyethylene glycol octylphenyl ether, 60-70 mM dithiothreitol, 1-2 mM phenylmethylsulfonyl fluoride, 1-2% v/v protease inhibitor, 50-100 mM Tris-Cl (pH 7.5). .
Adding dithiothreitol with a final concentration of 10-20 mM into 1mg of the protein sample obtained in the step (2), carrying out a water bath at 37-60 ℃ for 1-3 h, then adding iodoacetamide with a final concentration of 20-40 mM, carrying out a light-shielding reaction at 20-25 ℃ for 40-60min, adding a 4-fold volume of 50mM Tris-Cl (pH 8.1) buffer solution, and carrying out a reaction according to the protein: adding trypsin (trypsin) with the enzyme mass ratio of 50:1, and carrying out enzymolysis for 16 hours at the temperature of 37 ℃. And (3) freeze-drying the obtained peptide fragment at room temperature to obtain a treated proteome sample.
And (4) redissolving the peptide fragment obtained in the step (3) in 0.1% formic acid by volume concentration for RP LC-MS/MS analysis.
And (4) identifying a fragmentation spectrogram of the methylated peptide fragment in the mass spectrum data obtained in the step (4), performing spectral peak demethylation treatment, and further performing database search to determine a peptide fragment sequence.
Determining a methylation modification site by combining the peptide fragment sequence obtained in the step (5) and a spectrogram before demethylation;
the processing method is applied to high-efficiency analysis of the methylated proteomics, the sequence information of the corresponding methylated modified peptide fragment can be obtained, the result can be combined with subsequent site identification to determine the type of the methylated modification, and the method can be used for post-translational modified proteomics analysis.
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The invention is described in further detail below with reference to the following figures and embodiments:
FIG. 1 is a flow chart of a novel method of identifying protein methylation. The methylation sites were labeled with light methionine and heavy methionine, respectively, and the cells were disrupted to extract proteins, which were mixed at a ratio of 1:1 protein amount. Then carrying out enzyme digestion treatment and carrying out subsequent mass spectrometry; for fragmentation spectra of methylated peptide fragments that occur in pairs, the difference in molecular weight introduced by each methyl group is 3 Da; for fragmentation patterns of methionine-bearing peptide fragments occurring in pairs, the difference in molecular weight introduced per methionine was 4 Da. Thus, the two types of peptide fragments can be distinguished.
FIG. 2 shows the process of spectral peak demethylation. Judging the number of the contained methylated modification groups according to the molecular weight difference between the light standard spectrum peak and the heavy standard spectrum peak, and deducing the molecular weight of the spectrum peak of the corresponding non-modified peptide segment.
FIG. 3 is a library search result of a fragmentation spectrum of an unmodified peptide fragment deduced from a methylation modification spectrum and a fragmentation spectrum of a synthesized unmodified peptide fragment. The matching results of the two spectra are very close, and the effectiveness of the peak demethylation strategy is proved.
Detailed Description
The invention is further illustrated by the following examples, which are not intended to limit the scope of the invention.
Example 1
Peak demethylation strategy for scale-up analysis of methylated proteomics: HEK293 cells were cultured in DMEM medium containing 0.2mM L-methionine supplemented with 10% dialyzed fetal bovine serum for eight generations (at least eight generations) and containing 0.2mM L-methionine-carboxy-13C, methyl-D3Culturing for eight generations (at least eight generations) in the DMEM medium supplemented with 10% dialyzed fetal calf serum of (i); cells were harvested separately and disrupted separately in lysis buffer (8M urea, 1% v/v polyethylene glycol octylphenyl ether, 65mM dithiothreitol, 1mM phenylmethylsulfonyl fluoride, 1% v/v protease inhibitor, 50mM Tris-ClpH 7.5 buffer) with ultrasonic assistance; the light standard sample and the heavy standard sample are mixed according to the proportion of 1:1 of the protein amount. To 2mg of the protein mixture was added dithiothreitol to a final concentration of 20mM, and the mixture was incubated in a water bath at 37 ℃ for 2 hours, followed by addition of iodoacetamide to a final concentration of 40mM, and then reacted at 25 ℃ for 40 minutes in the absence of light, and 4 volumes of 50mM Tris-Cl (pH 8.1) buffer solution was added, in accordance with the protein: adding trypsin (trypsin) with the enzyme mass ratio of 50:1, carrying out enzymolysis for 16 hours at the temperature of 37 ℃, desalting the obtained peptide fragment sample, and freeze-drying at room temperature. Linear salt gradient over 36 min of the sample using strong cation exchange chromatography (Initial salt concentration 0mM KCl; stop salt concentration 250mM KCl) were divided into 36 fractions (one fraction per minute), desalted and lyophilized at room temperature, and the resulting peptide fragment was redissolved in 0.1% by volume formic acid for RPLC-MS/MS analysis. By identifying the spectrogram of the methylated peptide fragment in a mass spectrum file and carrying out spectral peak demethylation treatment, carrying out spectrogram search by using a human database (downloaded from Uniprot, http:// www.uniprot.org /) to determine the amino acid sequence of the modified peptide fragment, and further determining the modified sites by combining the spectrogram of the modified peptide fragment, 512 methylation results on 352 methylation sites are successfully identified, 10 methylation types except cysteine methylation types are covered, and the analysis method is proved to have strong applicability. The invention relates to a novel method for identifying protein methylation, develops a methylated peptide fragment analysis method which integrates stable isotope labeling of methionine cell culture amino acid, identifies and extracts a fragmentation spectrogram of a methylated peptide fragment and spectral peak demethylation treatment, and applies the methylated peptide fragment analysis method to the scale analysis of methylated proteome. This method does not require a preset type of modification and thus allows simultaneous analysis of multiple methylation events. The methylation identification method provides a new method and a new technical platform for the research and development of methylation proteomics.

Claims (10)

1. A method for identifying protein methylation, comprising:
(1) carrying out heavy labeling on a methylation modifying group in the protein by using a heavy-label methionine cell culture amino acid stable isotope labeling technology, and carrying out light-label labeling on the methylation modifying group in the protein by using a light-label methionine cell culture amino acid stable isotope labeling technology;
the cell culture system in the technology of stable isotope labeling of the amino acid in the cell culture of the re-labeled methionine contains 0.1-0.3 mM of L-methionine-carboxyl-13C, methyl-D3Adding dialyzed fetal calf serum with final volume concentration of 5-20%;
the cell culture system in the stable isotope labeling technology of the light-mark methionine cell culture amino acid is a DMEM culture medium containing 0.1-0.3 mM of L-methionine, and dialyzed fetal calf serum with final volume concentration of 5-20% is added;
(2) mixing the cells obtained in the step (1) according to the proportion of 1:1 of the number of the cells, and extracting protein, or mixing the cells according to the proportion of 1:1 of the amount of the protein after extracting the protein;
(3) carrying out Trypsin enzymolysis on the protein sample obtained in the step (2) and carrying out high-resolution mass spectrometry;
(4) identifying a fragmentation spectrogram of the methylated peptide fragment in the mass spectrum file obtained in the step (3), and performing spectral peak demethylation treatment on the fragmentation spectrogram to obtain a spectrogram of a corresponding non-modified peptide fragment; when identifying the spectrogram of the methylated peptide fragments, introducing the difference of the molecular weight of each methyl group into the spectrogram of a methylated peptide fragment source appearing in pairs, wherein the difference is 2.9-3.1 Da; for fragmentation patterns of methionine-containing peptide fragments occurring in pairs, the difference in molecular weight introduced per methionine is 3.9-4.1 Da;
(5) performing database search on the spectrogram obtained in the step (4) to determine the sequence of the peptide fragment;
(6) and (5) combining the peptide fragment sequence obtained in the step (5) and a spectrogram before demethylation to determine a methylation modification site.
2. The identification method according to claim 1, characterized in that:
the specific operation of the steps (1) and (2) is that the cells are respectively cultured in DMEM culture solution containing light mark methionine or heavy mark methionine; the obtained cells in the two labeling states are respectively subjected to ultrasonic-assisted disruption in a lysis solution and are mixed according to the mass ratio of 1:1 of the protein amount, or the obtained cells in the two labeling states are mixed in the lysis solution according to the mass ratio of 1:1 of the cell number and subjected to ultrasonic-assisted disruption.
3. The identification method according to claim 1, characterized in that:
the dialysis treatment is to remove molecules having a molecular weight of less than 10K Da.
4. The identification method according to claim 2, characterized in that:
the system of the lysis solution is 50-100 mM Tris-HCl buffer solution with pH value of 7.5 and containing 6-8M urea, 1-2% v/v polyethylene glycol octyl phenyl ether, 60-70 mM dithiothreitol, 1-2 mM phenylmethylsulfonyl fluoride, 1-2% v/v protease inhibitor.
5. The identification method according to claim 1, characterized in that:
the operation steps of the enzymolysis treatment in the step (3) are as follows: adding dithiothreitol with final concentration of 10-20 mM into protein sample, placing in water bath at 37-60 deg.C for 1-3 h, adding iodoacetamide with final concentration of 20-40 mM, reacting at 20-25 deg.C in dark place for 40-60min, adding 4-6 times volume of Tris-HCl buffer solution with pH value of 7.5-8.5 with 25-100 mM, and mixing according to protein: adding trypsin in a mass ratio of 50:1-100:1, and carrying out enzymolysis for 16-20 hours at 35-38 ℃.
6. The identification method according to claim 1, wherein: and (3) redissolving the obtained peptide fragment sample in formic acid for RP LC-MS/MS analysis.
7. The identification method according to claim 1, characterized in that:
the parent ionic molecular weight of the demethylated peptide fragment is the molecular weight of the methylated peptide fragment minus the methyl group.
8. The identification method according to claim 1, characterized in that:
in the successfully matched methylation spectrogram, secondary spectrum peaks are divided into two types, one type is a spectrum peak with the same molecular weight, the spectrum peak is a fragment ion which does not contain a methylation modification site, and the molecular weight of the spectrum peak is kept unchanged in a demethylation spectrum peak; the other is a spectrum peak of fixed molecular weight difference, the spectrum peak is a fragment ion containing a methylation modification site, and in the demethylated spectrum peak, the molecular weight of the spectrum peak is the molecular weight after subtracting a methyl group.
9. The identification method according to claim 1, characterized in that:
when identifying the fragmentation spectrogram of the methylated peptide fragment, the tolerance range of the deviation of the difference of the parent ion mass of the light spectrogram and the heavy spectrogram and the theoretical difference value is 5-10 p.p.m.; the tolerance range of the deviation of the retention time of the light standard peptide fragment and the heavy standard peptide fragment is +/-100 seconds; the tolerance range of the deviation of the parent ion signal intensity of the light standard peptide fragment and the heavy standard peptide fragment is within two times.
10. The identification method according to claim 1, characterized in that:
the cell is a HEK293 cell.
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CN111208244A (en) * 2018-11-22 2020-05-29 中国科学院大连化学物理研究所 Antibody-independent protein methylation modification enrichment analysis method
CN112852914B (en) * 2019-11-28 2023-01-13 中国科学院大连化学物理研究所 Method for weakening drug resistance of tumor cells
CN114994160B (en) * 2022-05-24 2023-09-15 天津医科大学 Analysis method for detecting formaldehyde-treated protein/polypeptide/amino acid food/product

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