WO2001002848A1 - Procede d'analyse multidimensionnelle d'un proteome - Google Patents
Procede d'analyse multidimensionnelle d'un proteome Download PDFInfo
- Publication number
- WO2001002848A1 WO2001002848A1 PCT/DE2000/002154 DE0002154W WO0102848A1 WO 2001002848 A1 WO2001002848 A1 WO 2001002848A1 DE 0002154 W DE0002154 W DE 0002154W WO 0102848 A1 WO0102848 A1 WO 0102848A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- methods
- proteins
- proteome
- separation
- identification
- Prior art date
Links
- 238000000034 method Methods 0.000 title claims abstract description 52
- 108010026552 Proteome Proteins 0.000 title claims abstract description 36
- 238000004141 dimensional analysis Methods 0.000 title abstract 2
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- 238000004445 quantitative analysis Methods 0.000 claims 1
- 230000035945 sensitivity Effects 0.000 claims 1
- 239000013543 active substance Substances 0.000 abstract description 3
- 235000018102 proteins Nutrition 0.000 description 62
- 210000004027 cell Anatomy 0.000 description 12
- 238000000539 two dimensional gel electrophoresis Methods 0.000 description 11
- 239000000499 gel Substances 0.000 description 10
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- DBMJMQXJHONAFJ-UHFFFAOYSA-M Sodium laurylsulphate Chemical compound [Na+].CCCCCCCCCCCCOS([O-])(=O)=O DBMJMQXJHONAFJ-UHFFFAOYSA-M 0.000 description 1
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Classifications
-
- 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
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2550/00—Electrophoretic profiling, e.g. for proteome analysis
Definitions
- the invention relates to a method for multidimensional analysis of a proteome, in which the biological tissue is digested with the proteome to be analyzed and the proteins belonging to the proteome are separated and quantitatively determined and identified.
- the method is used in biochemistry, in biotechnology, in medicine and in the pharmaceutical industry and serves u. a. for diagnostic purposes and for the development of biologically active substances. Special areas of application open up in basic research, for example to clarify developmental biological or cell-differentiating issues, as well as in applied research for the screening of drug banks, for the development and optimization of biologically active substances or for the differentiation between normal and pathogenic conditions in organisms.
- a gene of the genome can a) result from different processes, different types of mRNA which code for divergent proteins, and b) the proteins resulting from them can form a multitude of extraordinarily different functioning proteins through post-translational modification. Modifications known to date include phosphorylation and dephosphorylation, limited proteolysis, acetylation, methylation, adenylation, sulfation, glycosylation [McDonald LJ et al .: Enzymatic and nonenzymatic ADP-ribosylation of cysteine, Mol Cell Biochem, 1994 Sep, 138 (1-2 ), 221-6; Baenziger JU: Protein-specific glycosyltransferases: how and why they do it !, FASEB J, 1994 Oct, 8 (13), 1019-25; Mimnaugh EG et al .: The measurement of ubiquitin and ubiquitinated proteins, Electrophoresis, 1999 Feb.
- the cell structure, and descriptive amount is regulated in response to vertiv. and transmits the changes and information of the signals. DNA on the interactions with protein level. other cells. Quantity and activity are regulated.
- proteome that is, the entirety of all proteins in a cell with a certain level of development and under defined environmental conditions, represents a much more dynamic representation of the physiological state of cells, organs and organisms.
- the proteome analysis examines which parts of the genome under defined, cell-specific Conditions are expressed and modified. This led to rapidly growing interest in this area, with the consequence of increasing publication numbers (PubMed query search term: proteome; search 1 year ago: 64 entries, 2 years ago: 99 entries, 5 years ago: 122 entries), congresses and events this topic.
- the current procedure is as follows: In a first step, the biological materials have to be digested and homogenized (with exceptions: for example in the case of serum they are in a homogeneous solution). In the second step the proteins are separated, in the third the identification and in the fourth the evaluation of the data obtained [Ben RH et al .: Two dimensional electrophoresis, The State of the art and future directions, Proteome Research, New frontiers in functionel genomics, Springer 1997 Chap, 2, 13-33].
- Two-dimensional gel electrophoresis is currently used to separate the proteins of the proteome.
- First attempts with a two-dimensional HPLC have been made. So far, however, these have not achieved the selectivity of two-dimensional electrophoresis [Opiteck GJ, et al. Comprehensive two-dimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal biochem. 1998 May 1; 258 (2): 349-61.].
- the first dimension of two-dimensional electrophoresis is a separation according to the isoelectric point, i.e. ultimately according to the charge properties of a protein.
- the size of the proteins is separated in a denaturing sodium dodecyl sulfate gel.
- ampholytes required for the separation and the gel material acryl amide can lead to artifacts and thus contribute to misinterpretations that are difficult to identify
- Proteins which are present in very high concentrations give relatively strong signals and mask those which are present in low concentrations, so that direct identification and quantification is not possible in this case
- the loss of the native conformation in the denaturing separating gel causes the loss of the biologically functional properties and makes it difficult to identify the proteins by determining their biological properties, such as their catalytic activity or their specific binding properties
- the secondary analysis like the frequently used, specific proteolysis of individual proteins, followed by mass determination, makes an extraction step from the gel or from the blot membrane that is difficult to automate necessary.
- MALDI-MS matrix-assisted laser desorption ionization - mass spectrometry
- ESI-MS electrospray ionization - mass spectrometry
- the ESI technology can be quasi continuously connected to separation technologies and is currently showing a strong increase both in the development of the range of applications and in terms of technological possibilities.
- the enormous advances that have been achieved with both techniques in recent years allow mass resolutions up to isotope distribution, i.e. resolutions below 1 Dalton.
- a mass spectrum of peptide fragments is thus obtained after sequence-specific, defined protease digestion or another defined cleavage of the proteins. This spectrum is typical for every protein and is used for protein identification in sequence databases of proteins and expressed sequence tag banks.
- any post-translational modification of the proteins for example by glycosylation, interferes with the recognition.
- fragmentation spectra of the individual peptides in the mass spectrometer can provide information about the amino acid sequence of the peptides. This sequence information can be used alone or together with the other known data of the protein to identify it in a sequence database. This method for sequence analysis is currently not in use due to the difficulties of correct data interpretation Routine use. The limits of protein identification using mass spectrometric methods are the incomplete recording of all protein sequences in the existing databases.
- the characteristics of the individual proteins detected from the separation in 2-D electrophoresis such as the quantity, isoelectric point and size, and the data for protein identification from further steps, for example sequencing or mass spectrometry, are combined. This gives the picture of the totality of the proteins with their identity and quantity in the respective proteome.
- the object of the invention is to improve the quantification and identification of the proteins of a proteome, to facilitate them and to enable them for certain proteins in the first place.
- Advantageous embodiments of the method are listed in subclaims 2-12.
- the narrow quantity limitation due to the resilience of the 2-D electrophoresis used to date is no longer present.
- Amounts of protein in the range of a few grams can be used.
- the separation matrices can be used several times. This enables a higher reproducibility of the results.
- the sample material used is in the liquid phase and is therefore immediately accessible to subsequent analysis steps.
- analytical methods such as activity determination and immunological methods based on the native conformation of the analyte are possible.
- the separation of analytes with the same charge and size properties is not possible in the most commonly used 2-D electrophoresis.
- at least one further characteristic, such as the hydrophobicity of the analyte for the separation, this restriction does not apply.
- the samples are also available in the fractions for further preparative work after separation.
- Fig. 1 Separation of 1000 proteins in three dimensions
- Fig. 3a Fractions 68 to 100
- Fig. 2 Graphical three-dimensional representation of the fractions according to
- Fig. 1 As an exemplary embodiment, 1000 proteins are to be described by three properties A, B, C. These properties can be, for example, size, charge and hydrophobicity. The properties are distributed randomly in the proteins. All proteins are numbered consecutively. This is followed by a separation according to property A (for example the size), in which 100 fractions a with the corresponding proteins are obtained. These fractions a are separated into 10 fractions b according to property B (for example the charge).
- properties A for example the size
- property B for example the charge
- each of these fractions b is subjected to a separation according to property C (for example hydrophobicity) and gives fractions c.
- a total of 100 x 10 x 10 10,000 individual fractions are obtained.
- Each protein obtained by the separation is clearly assigned to one of the fractions a, b, c according to its properties.
- the respective fractions are designated by numbers.
- the fractions a belong to property A. They divide the possible value range of property A into one hundred identical parts each, i.e. H. for the assumption of a value range from 0 to 100, for example, the value 1 corresponds to the range 0 to 1, the value 2 to the range 1 to 2, -, the value 100 to the range 99-100.
- the possible value ranges of properties B and C are each divided into ten equal parts, i.e. H. for example, the value 1 corresponds to the range 1-10.
- every tenth fraction contains a protein.
- the possibility of multiple occupations results from the random analysis.
- the example shown in the list according to FIG. La-c contains 39 double assignments and a triple assignment of fractions.
- FIG. 2 shows a three-dimensional diagram with the positions of the fractions occupied by proteins according to FIG. 1.
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- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Molecular Biology (AREA)
- Hematology (AREA)
- Chemical & Material Sciences (AREA)
- Urology & Nephrology (AREA)
- Physics & Mathematics (AREA)
- Immunology (AREA)
- Biomedical Technology (AREA)
- Biophysics (AREA)
- Food Science & Technology (AREA)
- Biotechnology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Microbiology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Cell Biology (AREA)
- Medicinal Chemistry (AREA)
- Analytical Chemistry (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- General Physics & Mathematics (AREA)
- Pathology (AREA)
- Investigating Or Analysing Biological Materials (AREA)
Abstract
L'invention concerne un procédé d'analyse multidimensionnelle d'un protéome. Ce procédé trouve des applications dans la biochimie, dans la biotechnologie, dans la médecine ainsi que dans l'industrie pharmaceutique et sert, entre autres, à l'établissement de diagnostics et au développement de substances biologiquement actives. L'objectif de l'invention est d'améliorer et de faciliter, et, pour certaines protéines, principalement d'abord de permettre la quantification et l'identification des protéines d'un protéome. Selon l'invention, les protéines du protéome sont soumises, dans des conditions normalisées, à une pluralité n de procédés de séparation divers, de telle sorte que chacune des fractions m1 obtenue dans une étape de séparation donne, dans une étape de séparation m2 suivant immédiatement, des fractions liquides. Après n étapes de séparation, on est en présence de m1* m2*... mn = M fractions liquides qui, selon o procédés d'analyse différents, sont identifiées qualitativement et/ou quantitativement par des procédés d'identification connus en soi et déterminées quantitativement également par un procédé de quantification connu en soi, de telle sorte qu'après réunion des données d'analyse dans une banque de données, on obtient une image du protéome en n dimensions, caractérisée par des identificateurs et des quantificateurs, ainsi que par la position dans le réseau en n dimensions.
Priority Applications (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| GB0202280A GB2367894B (en) | 1999-07-05 | 2000-07-04 | Method for the multi-dimensional analysis of a proteome |
| DE10081888.9T DE10081888B4 (de) | 1999-07-05 | 2000-07-04 | Verfahren zur mehrdimensionalen Analyse eines Proteoms |
| AU65555/00A AU6555500A (en) | 1999-07-05 | 2000-07-04 | Method for the multi-dimensional analysis of a proteome |
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| DE1999132270 DE19932270A1 (de) | 1999-07-05 | 1999-07-05 | Verfahren zur mehrdimensionalen Analyse eines Proteoms |
| DE19932270.8 | 1999-07-05 |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| WO2001002848A1 true WO2001002848A1 (fr) | 2001-01-11 |
Family
ID=7914316
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/DE2000/002154 WO2001002848A1 (fr) | 1999-07-05 | 2000-07-04 | Procede d'analyse multidimensionnelle d'un proteome |
Country Status (4)
| Country | Link |
|---|---|
| AU (1) | AU6555500A (fr) |
| DE (2) | DE19932270A1 (fr) |
| GB (1) | GB2367894B (fr) |
| WO (1) | WO2001002848A1 (fr) |
Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2002040983A1 (fr) * | 2000-11-16 | 2002-05-23 | Basf Aktiengesellschaft | Procede de separation et de detection de proteines par electrophorese |
| WO2003019417A1 (fr) * | 2001-08-29 | 2003-03-06 | Bioinfomatix Inc. | Systeme et procede d'analyse du proteome et gestion de donnees |
| WO2003087834A2 (fr) * | 2002-04-08 | 2003-10-23 | Affinium Pharmaceuticals, Inc. | Purification, caracterisation et identification a haut rendement de proteines recombinantes |
Families Citing this family (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| AU2002338428A1 (en) * | 2001-04-20 | 2002-11-05 | Carnegie Mellon University | Methods and systems for identifying proteins |
Family Cites Families (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| KR20000036155A (ko) * | 1996-09-16 | 2000-06-26 | 스테판 제이 페이 | 이미지 분석 방법 및 장치 |
| EP0932882B1 (fr) * | 1996-10-25 | 2003-05-02 | Peter Mose Larsen | Analyse de proteome pour caracteriser des proteines a regulation positive et negative dans des echantillons biologiques |
-
1999
- 1999-07-05 DE DE1999132270 patent/DE19932270A1/de not_active Withdrawn
-
2000
- 2000-07-04 GB GB0202280A patent/GB2367894B/en not_active Expired - Fee Related
- 2000-07-04 WO PCT/DE2000/002154 patent/WO2001002848A1/fr active Application Filing
- 2000-07-04 AU AU65555/00A patent/AU6555500A/en not_active Abandoned
- 2000-07-04 DE DE10081888.9T patent/DE10081888B4/de not_active Expired - Fee Related
Non-Patent Citations (5)
| Title |
|---|
| BLACKSTOCK W P ET AL: "Proteomics: quantitative and physical mapping of cellular proteins", TRENDS IN BIOTECHNOLOGY,NL,ELSEVIER, AMSTERDAM, vol. 17, no. 3, March 1999 (1999-03-01), pages 121 - 127, XP004157732, ISSN: 0167-7799 * |
| DUCRET A ET AL: "HIGH THROUGHPUT PROTEIN CHARACTERIZATION BY AUTOMATED REVERSE-PHASE CHROMATOGRAPHY/ELECTROSPRAY TANDEM MASS SPECTROMETRY", PROTEIN SCIENCE,CAMBRIDGE UNIVERSITY PRESS, CAMBRIDGE,GB, vol. 7, no. 1, 7 March 1998 (1998-03-07), pages 706 - 719, XP000965234, ISSN: 0961-8368 * |
| LOPEZ M F: "Proteome analysis - I. Gene products are where the biological action is", JOURNAL OF CHROMATOGRAPHY B: BIOMEDICAL APPLICATIONS,NL,ELSEVIER SCIENCE PUBLISHERS, vol. 722, no. 1-2, 5 February 1999 (1999-02-05), pages 191 - 202, XP004156213, ISSN: 0378-4347 * |
| MOORE A W ET AL: "COMPREHENSIVE THREE-DIMENSIONAL SEPARATION OF PEPTIDES USING SIZE EXCLUSION CHROMATOGRAPHY/REVERSED PHASE LIQUID CHROMATOGRAPHY/ OPTICALLY GATED CAPILLARY ZONE ELECTROPHORESIS", ANALYTICAL CHEMISTRY,US,AMERICAN CHEMICAL SOCIETY. COLUMBUS, vol. 67, no. 19, 1 October 1995 (1995-10-01), pages 3456 - 3463, XP000535656, ISSN: 0003-2700 * |
| OPITECK G J ET AL: "COMPREHENSIVE TWO-DIMENSIONAL HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY FOR THE ISOLATION OF OVEREXPRESSED PROTEINS AND PROTEOME MAPPING", ANALYTICAL BIOCHEMISTRY,ACADEMIC PRESS, SAN DIEGO, CA,US, vol. 258, no. 2, 1 May 1998 (1998-05-01), pages 349 - 361, XP000960771, ISSN: 0003-2697 * |
Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2002040983A1 (fr) * | 2000-11-16 | 2002-05-23 | Basf Aktiengesellschaft | Procede de separation et de detection de proteines par electrophorese |
| WO2003019417A1 (fr) * | 2001-08-29 | 2003-03-06 | Bioinfomatix Inc. | Systeme et procede d'analyse du proteome et gestion de donnees |
| WO2003087834A2 (fr) * | 2002-04-08 | 2003-10-23 | Affinium Pharmaceuticals, Inc. | Purification, caracterisation et identification a haut rendement de proteines recombinantes |
| WO2003087834A3 (fr) * | 2002-04-08 | 2005-03-10 | Affinium Pharm Inc | Purification, caracterisation et identification a haut rendement de proteines recombinantes |
Also Published As
| Publication number | Publication date |
|---|---|
| GB2367894A (en) | 2002-04-17 |
| DE19932270A1 (de) | 2001-01-11 |
| AU6555500A (en) | 2001-01-22 |
| DE10081888A5 (de) | 2007-06-06 |
| DE10081888B4 (de) | 2014-02-06 |
| GB2367894B (en) | 2004-05-12 |
| GB0202280D0 (en) | 2002-03-20 |
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