CN111208243B - Anion exchange chromatographic column-based SUMO peptide fragment enrichment method - Google Patents
Anion exchange chromatographic column-based SUMO peptide fragment enrichment method Download PDFInfo
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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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Abstract
The invention relates to an enrichment method of SUMO peptide fragments based on an anion exchange chromatographic column, which comprises the following steps: performing enzyme digestion on protein alkaline sites, removing and retaining weak enzymolysis peptide fragments in an alkaline environment through an anion exchange chromatographic column, and collecting and retaining strong SUMO peptide fragment effluent liquid. Firstly, carrying out enzyme digestion on the basic site of the protein, wherein the SUMO peptide segment after enzyme digestion has a plurality of acidic amino acids, the retention of the SUMO peptide segment in an anion exchange chromatographic column is stronger than that of a non-SUMO peptide segment in an alkaline environment, eluting a digestion product with weaker retention by adopting the anion exchange chromatographic column, and finally collecting a peptide segment component with stronger retention, namely the enriched SUMO peptide segment. The method has the advantages of simple and convenient operation steps, high selectivity and high enrichment efficiency, can simultaneously enrich various types of SUMO peptide fragments, and improves the identification coverage of SUMO modification sites.
Description
Technical Field
The invention relates to an enrichment method of a SUMO peptide fragment, namely an enrichment method of the SUMO peptide fragment based on an anion exchange chromatographic column, so as to realize the high-efficiency and high-selectivity enrichment of the SUMO peptide fragment of a complex protein sample.
Background
Ubiquitination modification is one of the common post-translational modifications in organisms, and is the earliest discovered protein-associated modification, which plays an important role in protein degradation. Scientists have discovered successive ubiquitin-like proteins in the last decade, with small ubiquitin-like modifiers (SUMO) being the most attractive class. SUMO plays an important regulatory role in a variety of cellular physiological activities, such as maintenance of genomic stability, regulation of the cell cycle, regulation of cell differentiation and transcription factor activity, involvement in signal transduction, and the like. Many SUMO-modified proteins, such as transcription factors, are very low in abundance in cells, and only a small fraction of the protein substrate is modified under normal conditions. When mass spectrometry is carried out, the concentration range of proteins in a complex sample is wide, and high-abundance proteins can inhibit mass spectrum signals of low-abundance SUMO modified proteins. In addition, when the SUMO modified polypeptide (site) of the protein is analyzed, a large number of non-modified peptide fragments in the SUMO modified protein enzymolysis product generate great interference on the SUMO modified peptide fragments. The above factors seriously affect the efficiency of identification and quantification of the SUMO modified protein and its modified sites.
To improve the efficiency of identification of SUMO modifications, various biomarker-based enrichment methods have been developed. Generally, after His-tag labeling or mutation of SUMO, affinity enrichment of SUMO-modified proteins and polypeptides using nickel columns or antibodies (Nature Communication 2017,8, 14109; Nature Structural & Molecular Biology 2017,24, 325-336; Nature Communication
2015,6,7289). Such methods help to improve the efficiency of identification of SUMO modifications, but are only applicable to genetically altered biological samples (e.g., cells), and are ineffective for samples such as tissues, blood, etc.; furthermore, changes to the SUMO sequence may affect the properties and function of SUMO and therefore do not accurately reflect the true modification state of the protein in the sample. Several recent papers published in succession have reported successful identification of endogenous SUMO-modified peptides in human cells and mouse tissues (Nature Communication 2018,9, 2456; Nature Communication 2017,8, 1171; Molecular & Cellular proteins 2017, 16, 717-727), but still rely on expensive antibodies for affinity enrichment of SUMO-modified polypeptides and can only enrich for one type of SUMO-modified peptide. Therefore, there is a need to develop a universal enrichment method for endogenous SUMO modified proteins and modified polypeptides.
In order to overcome the problems of the methods, an efficient universal enrichment method is established, the characteristics of polyacid amino acids of the SUMO peptide fragments after alkaline site enzyme digestion are utilized, and anion exchange chromatography is combined to realize efficient removal of non-SUMO peptide fragments, so that the selectivity and efficiency of SUMO peptide fragment enrichment are improved.
Disclosure of Invention
The invention develops an enrichment method of the SUMO peptide fragment based on an anion exchange chromatographic column, which has simple and convenient operation steps, high selectivity and high enrichment efficiency
In order to realize the purpose, the technical scheme of the invention is as follows:
1) protein is enzymolyzed by adopting proteolytic enzyme with the enzyme cutting site of arginine or lysine carboxyl terminal
Performing denaturation, reduction and alkylation on protein, adding proteolytic enzyme for enzymolysis, wherein the dosage of the proteolytic enzyme is 1/5-1/100 of the mass of the protein, and performing enzymolysis for 2-48h at 25-45 ℃ to obtain a protein hydrolysate solution;
the proteolytic enzyme is one or more of trypsin, endoprotease Lys-C and endoprotease Arg-C.
2) Removing weakly retained enzymolysis peptide segment by anion exchange chromatography column in alkaline environment, collecting eluate of SUMO peptide segment with strong retention
Desalting the protein zymolyte solution, freeze-drying, dissolving by using phase A, loading the solution onto an anion exchange chromatographic column for separation at the flow rate of 0.1-3mL/min, and eluting under a low-salt concentration mobile phase to remove unreserved enzymolysis peptide segments, namely unreserved peptide segments when the molar concentration of sodium chloride is less than or equal to 100 mM; collecting the peptide fragment effluent under the mobile phase with high salt concentration, namely the peptide fragment effluent which is not retained when the molar concentration of sodium chloride is more than 100mM, desalting the solution, and freeze-drying to obtain the SUMO peptide fragment.
According to volume percentage concentration, phase A: 5-30% acetonitrile +1-10mM alkaline solution; phase B: 5% -30% acetonitrile +1-10mM alkaline solution + 200-.
The separation gradient of the anion exchange chromatographic column adopts a linear gradient or a step gradient.
The stationary phase of the anion exchange chromatographic column is a polymer matrix material (polyacrylate matrix, polystyrene matrix, polyacrylamide matrix) containing quaternary ammonium groups and/or tertiary amine groups in chemical bonding; the material may be a particulate material or a monolithic material;
the inner diameter of the chromatographic column is 1-8mm, and the length is 5-30 cm;
adjusting pH to alkaline environment, wherein the alkaline solution is one or more of ammonium bicarbonate buffer salt solution with pH of 8-14, phosphate buffer salt solution with pH of 8-14, tris buffer salt solution with pH of 8-14, ammonia water, sodium carbonate solution or sodium hydroxide solution; the buffer concentration is 1-10 mM.
The invention has the beneficial effects that:
1. the alkaline protease has high enzyme cutting efficiency and good selectivity;
2. the separation capacity of anion exchange chromatography is strong, and the high-efficiency removal of non-SUMO peptide fragments is promoted;
3. the different types of SUMO peptide fragments are not distinguished, so that the loss of the SUMO peptide fragments is avoided;
the invention has the advantages of high enrichment selectivity and high enrichment efficiency, can simultaneously enrich various types of SUMO peptide fragments, and improves the identification coverage of SUMO modification sites.
Drawings
FIG. 1: enrichment process of SUMO peptide fragment;
FIG. 2: chromatographic peak of trypsin-digested SUMO1 standard peptide in anion exchange chromatographic column (SUMO1 standard peptide sequence: ELGMEEEDVIEVYQEQTGG (19) -LLVHMGLLKSEDKVK (9));
FIG. 3 shows the chromatographic peaks of mixtures of trypsin-cleaved SUMO1 standard peptide and 4 common standard peptides in an anion exchange chromatography column (4 standard peptide sequences: LIGNFQLTGIAPAPK; LNLFTGWK; VLIAAHGNSLR; GVVGIVAGGGR);
FIG. 4: chromatographic peak of the trypsinized HeLa holoprotein sample in an anion exchange chromatographic column.
Wherein FIG. 4(a) is the chromatographic peak in an anion exchange chromatography column of the trypsinized HeLa whole protein sample of example 6; FIG. 4(b) is the chromatographic peak in anion exchange chromatography column of the trypsinized HeLa whole protein sample of example 7;
Detailed Description
Example 1
As shown in fig. 1, firstly, the basic site of the protein is enzyme-cut, the enzyme-cut SUMO peptide fragment has a plurality of acidic amino acids, and the retention in the anion exchange chromatography is stronger than that of the non-SUMO peptide fragment in the alkaline environment, the anion exchange chromatography is adopted to elute the enzyme-cut product with weaker retention, and finally, the peptide fragment component with stronger retention is collected, namely the enriched SUMO peptide fragment.
Taking HeLa cells as a sample, dissolving 100 mu g of extracted protein in 100 mu l of 50mM ammonium bicarbonate buffer solution (pH is 8) of 8M urea, adding 10 mu l of 100mM dithiothreitol, performing denaturation and reduction at 56 ℃ for 1h, adding 10 mu l of 300mM iodoacetamide for reaction for 0.5h, adding 30 mu l of 100mM dithiothreitol, performing incubation for 10min, performing enzyme digestion by trypsin, wherein the enzyme dosage is 1/10 based on the mass of the sample, the temperature is 37 ℃, performing enzymolysis for 60min, removing salt, performing freeze-drying, re-dissolving in 0.1% formic acid, and performing mass spectrometry, wherein lysine and arginine at the carboxyl end of a peptide segment are efficiently and selectively sheared.
Example 2
Taking HeLa cells as a sample, dissolving 100 mu g of extracted protein in 100 mu l of 50mM ammonium bicarbonate buffer solution (pH is 8) of 8M urea, adding 10 mu l of 100mM dithiothreitol, performing denaturation and reduction at 56 ℃ for 1h, adding 10 mu l of 300mM iodoacetamide for reaction for 0.5h, adding 30 mu l of 100mM dithiothreitol, incubating for 10min, performing enzyme digestion by Lys-C, wherein the enzyme dosage is 1/10 based on the mass of the sample, the temperature is 37 ℃, performing enzymolysis for 60min, removing salt, freeze-drying, re-dissolving in 0.1% formic acid, performing mass spectrometry, and shearing lysine at the carboxyl end of a peptide segment with high efficiency and high selectivity.
Example 3
Taking HeLa cells as a sample, dissolving 100 mu g of extracted protein in 100 mu l of 50mM ammonium bicarbonate buffer solution (pH is 8) of 8M urea, adding 10 mu l of 100mM dithiothreitol, performing denaturation and reduction at 56 ℃ for 1h, adding 10 mu l of 300mM iodoacetamide for reaction for 0.5h, adding 30 mu l of 100mM dithiothreitol, incubating for 10min, performing enzyme digestion by Arg-C, wherein the enzyme dosage is 1/10 based on the mass of the sample, the temperature is 37 ℃, performing enzymolysis for 60min, removing salt, freeze-drying, re-dissolving in 0.1% formic acid, performing mass spectrometry, and shearing arginine at the carboxyl end of a peptide segment efficiently and selectively.
Example 4
Mu.g of SUMO1 standard peptide was redissolved in phase A and loaded onto a tertiary amino ion exchange column (4.6mm i.d. times.15 cm) for gradient elution, elution gradient: 0-20min, 5% B-25% B; 20-30min, 25% B isocratic; 30.1-50min, and isocratic elution of 50% B, wherein the flow rate is 0.5 mL/min. Phase A: 20% acetonitrile +1mM pH 8Tris buffer; phase B: 20% acetonitrile +1mM Tris buffer pH 8 +500mM sodium chloride. As shown in FIG. 2, after 30min of the fraction not retained before elution, the 30min post-SUMO 1 standard peptide fraction was collected, desalted and lyophilized. The SUMO1 peptide fragment is effectively enriched and identified by mass spectrometry after being dissolved in 0.1% formic acid.
Example 5
Mu.g of SUMO1 standard peptide was mixed with 4 common standard peptides, redissolved in phase A and loaded onto a tertiary amine based ion exchange column (4.6mm i.d.. times.15 cm) for gradient elution, elution gradient: 0-20min, 5% B-25% B; 20-30min, 25% B isocratic; 30.1-50min, and isocratic elution of 50% B, wherein the flow rate is 0.5 mL/min. Phase A: 20% acetonitrile +1mM pH 8Tris buffer; phase B: 20% acetonitrile +1mM Tris buffer pH 8 +500mM sodium chloride. As shown in FIG. 3, 30min after elution without retention of peptide fragments, 30min after the collection of the SUMO1 standard peptide fraction, desalting, and freeze-drying. The SUMO1 peptide fragment is effectively enriched and identified by mass spectrometry after being dissolved in 0.1% formic acid.
Example 6
Taking HeLa cells as a sample, dissolving 1000 mu g of extracted protein in 100 mu l of 50mM ammonium bicarbonate buffer solution (pH is 8) of 8M urea, adding 10 mu l of 100mM dithiothreitol, performing denaturation reduction at 56 ℃ for 1h, adding 10 mu l of 300mM iodoacetamide for reaction for 0.5h, adding 30 mu l of 100mM dithiothreitol, performing incubation for 10min, performing enzyme digestion by adopting trypsin, wherein the enzyme dosage is 1/10 based on the mass of the sample, the temperature is 37 ℃, performing enzymolysis for 60min, removing salt, and performing freeze-drying. Redissolved in phase A and applied to a tertiary amine ion exchange column (4.6mm i.d. 15cm) for gradient elution, elution gradient: 0-25min, 5% B-30% B; 25-45min, 30% B isocratic; 45.1-65min, and 80% B isocratic elution with a flow rate of 0.5 mL/min. Phase A: 20% acetonitrile +1mM pH 8Tris buffer; phase B: 20% acetonitrile +1mM Tris buffer pH 8 +500mM sodium chloride. As shown in FIG. 4(a), the peptide fragments which are not retained 45min before elution are collected, and the 45min later fractions are desalted and lyophilized. And (3) the peptide fragments are re-dissolved in 0.1% formic acid to be subjected to mass spectrometry, so that the SUMO peptide fragments are effectively enriched and identified and analyzed.
Example 7
Taking HeLa cells as a sample, dissolving 1000 mu g of extracted protein in 100 mu l of 50mM ammonium bicarbonate buffer solution (pH is 8) of 8M urea, adding 10 mu l of 100mM dithiothreitol, performing denaturation reduction at 56 ℃ for 1h, adding 10 mu l of 300mM iodoacetamide for reaction for 0.5h, adding 30 mu l of 100mM dithiothreitol, performing incubation for 10min, performing enzyme digestion by adopting trypsin, wherein the enzyme dosage is 1/10 based on the mass of the sample, the temperature is 37 ℃, performing enzymolysis for 60min, removing salt, and performing freeze-drying. Redissolved in phase A and applied to a tertiary amine ion exchange column (4.6mm i.d. 15cm) for gradient elution, elution gradient: 0-25min, 5% B-25% B; 25-50min, 25% B isocratic; 50.1-70min, and isocratic elution with 50% B; 70.1-90min, and 100% B isocratic elution with flow rate of 0.5 mL/min. Phase A: 20% acetonitrile +1mM pH 8Tris buffer; phase B: 20% acetonitrile +1mM Tris buffer pH 8 +500mM sodium chloride. As shown in FIG. 4(b), the peptide fragments which are not retained 50min before elution are collected, and the fractions 50min after elution are desalted and lyophilized. And (3) the peptide fragments are re-dissolved in 0.1% formic acid to be subjected to mass spectrometry, so that the SUMO peptide fragments are effectively enriched and identified and analyzed.
Claims (8)
1. An enrichment method of SUMO peptide fragments based on an anion exchange chromatographic column is characterized by comprising the following steps: the method comprises the following steps: 1) Carrying out enzyme digestion on protein alkaline sites; 2) Anion exchange chromatography column separation: removing the weakly retained enzymolysis peptide fragment by an anion exchange chromatographic column in an alkaline environment, and collecting the effluent liquid of the strongly retained SUMO peptide fragment;
wherein the step 2) of collecting and retaining the effluent liquid of the stronger SUMO peptide fragment comprises the following specific steps: after the peptide fragments which are not retained in the low-salt concentration mobile phase are eluted, collecting the peptide fragment effluent in the high-salt concentration mobile phase, namely the peptide fragment effluent which is not retained when the molar concentration of sodium chloride is more than 100mM, desalting the solution, and freeze-drying to obtain the SUMO peptide fragments; the method comprises the following steps of removing and retaining weak enzymolysis peptide fragments in an alkaline environment through an anion exchange chromatographic column: desalting the protein zymolyte solution, freeze-drying, dissolving by using phase A, loading the solution onto an anion exchange chromatographic column for separation at the flow rate of 0.1-3mL/min, and eluting under a mobile phase with low salt concentration to remove unreserved enzymolysis peptide segments, namely unreserved peptide segments when the molar concentration of sodium chloride is less than or equal to 100 mM; according to volume percentage concentration, phase A: 5-30% acetonitrile +1-10mM alkaline solution; phase B: 5% -30% acetonitrile +1-10mM alkaline solution +200 mM sodium chloride.
2. The enrichment method according to claim 1, wherein: the protein alkaline site enzyme digestion comprises the following specific steps: adding proteolytic enzyme into the protein sample solution after denaturation, reduction and alkylation for enzymolysis, wherein the dosage of the proteolytic enzyme is 1/5-1/100 of the mass of the protein, the enzymolysis time is 2-48h, and the enzymolysis temperature is 25-45 ℃, so as to obtain the protein hydrolysate solution.
3. The enrichment method according to claim 1, wherein: the separation gradient of the anion exchange chromatographic column adopts a linear gradient or a step gradient.
4. A method according to claim 1 or 2, characterized in that: the proteolytic enzyme is one or more of trypsin, endoprotease Lys-C and endoprotease Arg-C.
5. A method according to claim 1 or 3, characterized by: the stationary phase of the anion exchange chromatographic column is a polymer matrix material containing quaternary ammonium groups and/or tertiary amine groups which are chemically bonded; the material may be a particulate material or a monolithic material; the chromatographic column has an inner diameter of 1-8mm and a length of 5-30 cm.
6. The method of claim 1, wherein: adjusting pH to alkaline environment, wherein the alkaline solution is one or more of ammonium bicarbonate buffer salt solution with pH of 8-14, phosphate buffer salt solution with pH of 8-14, tris buffer salt solution with pH of 8-14, ammonia water, sodium carbonate solution or sodium hydroxide solution; the buffer concentration is 1-10 mM.
7. The method of claim 5, wherein: the polymer matrix material comprises one or more than two of polyacrylate matrix, polystyrene matrix and polyacrylamide matrix.
8. The method according to claim 1, which is applicable to the enrichment and identification of sumoylated modified protein 2 and peptide fragments in biological samples; the biological sample is one or more of cells, tissues and body fluid.
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