Multiplex proteome quantification method based on isobaric dimethyl labeling

Abstract

A multiplex proteome quantification method based on isobaric dimethyl labeling implements dimethyl labeling of peptide N-terminal in an acidic condition and C-terminal in an alkaline condition one after another by means of Hall the property that a dimethylation reaction has different rates on an amino group at the peptide N-terminal and an amino group on a Lysine side chain at the peptide C-terminal in the acidic condition. Multiplex labeling of peptide samples is implemented by means of the organic combination of various isotope forms of a dimethyl labeling reagents. The mass-to-charge ratios in MS1 of peptides after multiplex labeling are completely the same, the mass-to-charge ratios of the fragment ions in MS2 are different, and multiplex quantitative analyses are carried out by extracting the intensity values of corresponding fragment ions in the MS2.

Claims

1. A multiplex proteome quantification method, comprising: digesting a protein into a plurality of peptides using a protease that cleaves at a carboxyl side of lysine; and performing dimethyl labeling of a peptide among the plurality of peptides to produce a plurality of labeled peptides, wherein the dimethyl labeling comprises: performing a first dimethyl labeling to a peptide N-terminal under a first acidic condition using a first dimethyl labeling reagent and the second dimethyl labeling to a peptide C-terminal on a Lysine side chain under a first alkaline condition using a second dimethyl labeling reagent to form a first labeled peptide; performing a third dimethyl labeling to a peptide N-terminal under a second acidic condition using a third dimethyl labeling reagent and a fourth dimethyl labeling to a peptide C-terminal on a Lysine side chain under a second alkaline condition using a fourth dimethyl labeling reagent to form a second labeled peptide; performing a fifth dimethyl labeling to a peptide N-terminal under a third acidic condition using a fifth dimethyl labeling reagent and a sixth dimethyl labeling to a peptide C-terminal on a Lysine side chain under a third alkaline condition using a sixth dimethyl labeling reagent to form a third labeled peptide, wherein each of the first dimethyl labeling reagent, the second dimethyl labeling reagent, the third dimethyl labeling reagent, the fourth dimethyl labeling reagent, the fifth dimethyl labeling reagent, and the sixth dimethyl labeling reagent comprises a first compound selected from CH.sub.2O, .sup.13CH.sub.2O, CD.sub.2O, and .sup.13CD.sub.2O, and a second compound selected from NaBH.sub.3CN and NaBD.sub.3CN, and the plurality of labeled peptides have a same mass-to-charge ratio; ionizing the plurality of labeled peptides and acquiring ionized forms of the plurality of labeled peptides in MS1 of a mass spectrometer; separating and fragmenting the ionized forms of the plurality of labeled peptides and acquiring fragment ions in MS2 of the mass spectrometer; and performing multiplex quantitative analysis based on intensities of the fragment ions in the MS2.

2. The method according to claim 1, wherein the plurality of labeled peptides further comprises a fourth labeled peptide, or the fourth labeled peptide and a fifth labeled peptide, or the fourth labeled peptide, the fifth labeled peptide, and a sixed labeled peptide, wherein the first to the sixth dimethyl labeling reagents are selected from a reagent comprising .sup.13CH.sub.2O and NaBH.sub.3CN, a reagent comprising CD.sub.2O and NaBD.sub.3CN, a reagent comprising CD.sub.2O and NaBH.sub.3CN, a reagent comprising .sup.13CH.sub.2O and NaBD.sub.3CN, a reagent comprising .sup.13CD.sub.2O and NaBH.sub.3CN, a reagent comprising CH.sub.2O and NaBD.sub.3CN, a reagent comprising CH.sub.2O and NaBD.sub.3CN, a reagent comprising .sup.13CD.sub.2O and NaBH.sub.3CN, a reagent comprising .sup.13CH.sub.2O and NaBD.sub.3CN, a reagent comprising CD.sub.2O and NaBH.sub.3CN, a reagent comprising CD.sub.2O and NaBD.sub.3CN, and a reagent comprising .sup.13CH.sub.2O and NaBH.sub.3CN.

3. The analysis method according to claim 2, comprising displaying a spectrum of each of the plurality of labeled peptides on a same spectrum of MS2; extracting and summing up intensity values of fragment ions of a, b and y for each of the plurality of labeled peptides on the MS2; assigning the sum of intensity values of fragment ions of a, b and y as an intensity of the corresponding labeled peptide; and comparing the intensity of each of the plurality of labeled peptides.

4. The method according to claim 2, wherein the protein is denatured, reduced, alkylated and then is incubated by the protease.

5. The method according to claim 1, wherein the mass spectrometer comprises an Orbitrap analyzer, or a TOF analyzer, or an FT-ICR analyzer.

6. The method according to claim 1, wherein the protease is a Lys-C protease.

7. The method according to claim 1, performing a first dimethyl labeling proceeds the second dimethyl labeling.

8. The method according to claim 1, wherein, in each of the first acidic condition, the second acidic condition, and the third acidic condition, a pH value is 2.0 to 5.0 and a labeling time is 5 to 120 min.

9. The method according to claim 1, wherein, in each of the first alkaline condition, the second alkaline condition, and the third alkaline condition, a pH value is 7.5 to 12 and a labeling time is 5 to 120 min.

Description

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

(1) FIG. 1 is a schematic diagram of isobaric dimethyl labeling;

(2) FIG. 2 is a theory mass spectrum diagram of the mixture of the labeling of six samples; and

(3) FIG. 3 is a diagram of equivalently mixed quantitative results of six samples. The figure shows results obtained by taking the log 2 for the quantitative ratio after the six samples are mixed in a ratio of 1:1:1:1:1:1.

DETAILED DESCRIPTION OF THE EMBODIMENTS

Embodiment 1

(4) 1. Protein Digestion

(5) The protein samples are dissolved in 8 M urea solution, and the DTT is added to reach the final concentration of 10 mM, then the samples are denatured and reduced at 56° C. for 1 h, and the IAA is added to reach the final concentration of 20 mM, and the samples are kept in the dark at room temperature for 30 min, and then the urea solution is then diluted to 1 M. Finally, the Lys-C is added to the samples in a ratio of 1:50 (enzyme/protein, w/w), and the samples are digested at 37° C. overnight. The samples are desalted by C18 trap column and lyophilized, and then resolved with water.

(6) 2. Dimethyl Labeling of Peptides

(7) The sextuple dimethyl labeling is separately carried out on the peptides. As shown in Table 3, the specific labeling methods are as follows:

(8) The first labeling: The peptide digests are loaded on a C18-trap column and firstly balanced by 1.5% (v/v) CH.sub.3COOH aqueous solution of the acid solution. The dimethyl labeling is selectively carried out on an amino group at peptide N-terminal in the acid solution, and the labeling solution is obtained by adding 50 μL of 4% (v/v).sup.13CH.sub.2O and 50 μL of 0.6 M (w/v) NaBH.sub.3CN to 1 mL 1.5% (v/v) CH.sub.3COOH aqueous solution for 20 min with the flow rate of 50 μL/min. The trap column is then washed with 1.5% (v/v) CH.sub.3COOH aqueous solution of the acid solution and water, and then is balanced by the phosphate buffer with pH value of 8.0 of the alkaline solution. The dimethyl labeling is carried out on an amino group on a Lysine side chain at peptide C-terminal in the alkaline condition, and the labeling solution is obtained by adding 50 μL of 4% (v/v) CD.sub.2O and 50 μL of 0.6 M (w/v) NaBD.sub.3CN to 1 mL phosphate buffer with pH value of 8.0 for 10 min with the flow rate of 50 μL/min. Finally, the trap column is washed with the phosphate buffer solution with pH value of 8.0 of the alkaline solution and water in sequence; and finally the sample is eluted with 80% (v/v) ACN from the trap column.

(9) The second labeling: The labeling method is the same as the first labeling. The labeling solution in an acidic condition is changed to the solution obtained by adding 50 μL of 4% (v/v) CD.sub.2O and 50 μL of 0.6 M (w/v) NaBH.sub.3CN to 1 mL 1.5% (v/v) CH.sub.3COOH aqueous solution. The labeling solution in an alkaline condition is changed to the solution obtained by adding 50 μL of 4% .sup.13CH.sub.2O and 50 μL of 0.6 M (w/v) NaBD.sub.3CN to 1 mL phosphate buffer solution with pH value of 8.0.

(10) The third labeling: The labeling method is the same as the first labeling. The labeling solution in an acidic condition is changed to the solution obtained by adding 50 μL of 4% (v/v).sup.13CD.sub.2O and 50 μL of 0.6 M (w/v) NaBH.sub.3CN to 1 mL 1.5% (v/v) CH.sub.3COOH aqueous solution. The labeling solution in an alkaline condition is changed to the solution obtained by adding 50 μL of 4% (v/v) CH.sub.2O and 50 μL of 0.6 M (w/v) NaBD.sub.3CN to 1 mL phosphate buffer solution with pH value of 8.0.

(11) The fourth labeling: The labeling method is the same as the first labeling. The peptide digests are loaded on a C18-trap column and firstly balanced by 1.5% (v/v) CH.sub.3COOH D.sub.2O solution of the acid solution. The dimethyl labeling is selectively carried out on an amino group at peptide N-terminal in the acid solution, and the labeling solution is obtained by adding 50 μL of 4% (v/v) CH.sub.2O and 50 μL of 0.6 M (w/v) NaBD.sub.3CN to 1 mL 1.5% (v/v) CH.sub.3COOH D.sub.2O solution for 30 min with the flow rate of 25 μL/min. The trap column is then washed with 1.5% CH.sub.3COOH aqueous solution of the acid solution and water in sequence, and then is balanced by the phosphate buffer solution with pH value of 8.0 of the alkaline solution. The dimethyl labeling is carried out on an amino group on a Lysine side chain at peptide C-terminal in the alkaline condition, and the labeling solution is obtained by adding 50 μL of 4% (v/v).sup.13CD.sub.2O and 50 μL of 0.6 M (w/v) NaBH.sub.3CN to 1 mL phosphate buffer solution with pH value of 8.0 for 10 min with the flow rate of 50 μL/min. Finally, the trap column is washed with the phosphate buffer solution with pH value of 8.0 of the alkaline solution and water in sequence; and finally the sample is eluted with 80% (v/v) ACN from the trap column.

(12) The fifth labeling: The labeling method is the same as the fourth labeling. The labeling solution in an acidic condition is changed to the solution obtained by adding 50 μL of 4% (v/v).sup.13CH.sub.2O and 50 μL of 0.6 M (w/v) NaBD.sub.3CN to 1 mL 1.5% (v/v) CH.sub.3COOH D.sub.2O solution. The labeling solution in an alkaline condition is changed to the solution obtained by adding 50 μL of 4% (v/v) CD.sub.2O and 50 μL of 0.6 M (w/v) NaBH.sub.3CN to 1 mL phosphate buffer solution with pH value of 8.0.

(13) The sixth labeling: The labeling method is the same as the fourth labeling. The labeling solution in an acidic condition is changed to the solution obtained by adding 50 μL of 4% (v/v) CD.sub.2O and 50 μL of 0.6 M (w/v) NaBD.sub.3CN to 1 mL 1.5% (v/v) CH.sub.3COOH D.sub.2O solution. The labeling solution in an alkaline condition is changed to the solution obtained by adding 50 μL of 4% (v/v).sup.13CH.sub.2O and 50 μL of 0.6 M (w/v) NaBH.sub.3CN to 1 mL phosphate buffer solution with pH value of 8.0.

(14) All the samples are lyophilized and then resolved to the mass concentration of 0.5 mg/mL with buffer solution A (containing aqueous solution of 2% (v/v) ACN and 0.1% (v/v) FA). The samples are mixed with fixed ratios to be for MS analysis.

(15) 3. LC-MS Analysis.

(16) Liquid chromatography condition: Mobile phases are buffer solution A (containing aqueous solution of 2% (v/v) ACN and 0.1% (v/v) FA) and buffer solution B (containing aqueous solution of 98% (v/v) water and 0.1% (v/v) FA). The gradient separation is performed using buffer solution B with a gradient of 0% for 10 min, the linear gradient separation is performed using buffer solution B with a gradient of 5% to 25% for 125 min, and then the linear gradient separation is performed using buffer solution B with a gradient of 25% to 35% for 10 min at a flow rate of 300 nL/min.

(17) Mass acquisition condition: A Q-Exactive MS is used, and a data-dependent acquisition (DDA) mode is used. The resolution of Full MS is 70000 (m/z=200), and the mass range is from 350 to 1800 m/z. Ten most intensive ions are selected for MS/MS fragmentation. The dynamic exclusion time is 20 s. The activation type is HCD, a normalized collision energy is 28%, a isolation window is 2.0 Da, fixed first mass of the MS2 is 50.0 Da, and the resolution of MS/MS is 35000 (m/z=200). Each sample above is injected in parallel for three times.

(18) 4. Data Analysis

(19) The acquired raw files by MS use a MaxQuant (v1.2.2.5) software package, and use Andromeda as database search engine, to conduct database search. The fixed modification is set as cysteine carbamidomethylation; and the variable modification is set as acetyl (Protein N-term), oxidation (M), N-term and K respectively select the corresponding dimethyl labeling modifications. The human protein database is downloaded from ftp.uniprot.org on July, 2013. The mass tolerance of the MS1 is 6 ppm, and the mass tolerance of the MS2 is 20 ppm. The protease is Lys-C. Two missed cleavage sites are allowed. The FDRs less than 0.01 for proteins and peptides are required. For quantitative analysis, the identified peptides are theoretically fragmented and matched with the corresponding mgf files to extract all the eligible fragment ions. Then the ion pairs are matched, the appeared ion of each sample is kept, and then most of all the fragment ion intensities of the labeling are summed as the ion intensity of the peptide. The ion intensities of multiplex labeled peptides are compared in pairs as relative quantitative ratios of identified peptides of the spectra. The median of the spectra matching the same peptide is taken as a quantitative result of the peptide, and the medians of all identified peptides for the same protein are taken as a quantitative result of the protein. All the results of three replicates are combined, and the values of the same protein are averaged as the final quantitative result of the protein. All the analyses are completed by SPSS (v20) and Excel (v2010).

(20) Method Evaluation:

(21) 1. Six samples are mixed in a ratio of 1:1:1:1:1:1. The quantitative coverage is more than 95%. The simultaneous quantitative analysis of six protein samples can be implemented. The quantitative accuracy and precision results are shown in Table 1 and FIG. 3. The quantitative results are close to the theoretical values with high precision.

(22) 2. Wide quantitative dynamic range: The samples are mixed in a ratio of 1:2:5:10:20:50. The results are shown in Table 2. This method can achieve dynamic ranges of 50-fold with good quantitative accuracy, and doesn't have underestimated effect based on a reporter ion quantitative method, which is due to the fact that the method is based on a quantitative method of multiple fragment ions of the MS2, thereby effectively reducing the quantitative interference of the co-eluted peptides.

Embodiment 2

(23) The labeling process is carried out in a centrifuge tube. After the labeling in an acidic condition, the solvent is exchanged by a C18-trap column. Then the labeling in an alkaline condition is carried out after elution. The other processes are the same as those in Embodiment 1.

Embodiment 3

(24) The labeling process in the acidic condition is carried out in a centrifuge tube. After the solvent is exchanged by the C18-trap column, the labeling in the alkaline condition is carried out on the trap column. The other processes are the same as those in Embodiment 1.

Embodiment 4

(25) The dimethyl labeling is selectively carried out on the amino group at the peptide N-terminal in the acidic condition, and the labeling solution comprises 1% (v/v) CH.sub.3COOH aqueous solution, 4% (v/v) CH.sub.2O aqueous solution and isotopic forms thereof, and 0.6 M (w/v) NaBH.sub.3CN solution and isotopic forms thereof. The labeling time is 10 min. The other processes are the same as those in Embodiment 1.

Embodiment 5

(26) The quadruple labeling is achieved by using the first four labeling methods in Embodiment 1. The other processes are the same as those in Embodiment 1.

(27) TABLE-US-00001 TABLE 1 Quantitative accuracy and precision results of six equivalently mixed samples 30H/30L 32L/30L 32H/30L 34L/30L 34H/30L Average 0.92 1.20 0.96 0.98 1.03 RSD/% 14 16 14 14 14

(28) TABLE-US-00002 TABLE 2 Quantitative results of dynamic range Theoretical ratio (Heavy/Light Labeling) 2 5 10 20 50 Experimental ratio 2.54 5.34 13.28 21.39 53.00 (Heavy/Light Labeling)

(29) TABLE-US-00003 TABLE 3 Sextuple labeling methods Flow rate Flow rate Mass increase of Labeling and time for Labeling and time for both terminals Multi- Abbrev- reagent of labeling of reagent of labeling of (N-terminal- plicities iation N-terminal N-terminal K-terminal K-terminal K-terminal/Da) 1 2L-6H .sup.13CH.sub.2O + 20 min CD.sub.2O + 10 min 30.03801-34.06896 NaBH.sub.3CN 50 μL/min NaBD.sub.3CN 50 μL/min 2 4H-4L CD.sub.2O + .sup.13CH.sub.2O + 32.05641-32.05056 NaBH.sub.3CN NaBD.sub.3CN 3 6L-2H .sup.13CD.sub.2O + CH.sub.2O + 34.06312-30.04385 NaBH.sub.3CN NaBD.sub.3CN 4 2H-6L CH.sub.2O + 30 min .sup.13CD.sub.2O + 30.04385-34.06312 NaBD.sub.3CN 25 μL/min NaBH.sub.3CN 5 4L-4H .sup.13CH.sub.2O + CD.sub.2O + 32.05056-32.05641 NaBD.sub.3CN NaBH.sub.3CN 6 6H-2L CD.sub.2O + .sup.13CH.sub.2O + 34.06896-30.03801 NaBD.sub.3CN NaBH.sub.3CN

(30) The method has advantages of high accuracy, good precision, and wide dynamic range, which can simultaneously implement the simultaneous quantitative analysis of six protein samples, thereby greatly improving the throughput of the quantitative analysis of proteins and saving the analysis time.