Bottom-up proteomics is a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry.[1][2] The major alternative workflow used in proteomics is called top-down proteomics where intact proteins are purified prior to digestion and/or fragmentation either within the mass spectrometer or by 2D electrophoresis.[3] Essentially, bottom-up proteomics is a relatively simple and reliable means of determining the protein make-up of a given sample of cells, tissues, etc.[4]
Top-down vs bottom-up proteomics
In bottom-up proteomics, the crude protein extract is enzymatically digested, followed by one or more dimensions of separation of the peptides by liquid chromatography coupled to mass spectrometry, a technique known as shotgun proteomics.[5][6] By comparing the masses of the proteolytic peptides or their tandem mass spectra with those predicted from a sequence database or annotated peptide spectral in a peptide spectral library, peptides can be identified and multiple peptide identifications assembled into a protein identification.
For high throughput bottom-up methods, there is better front-end separation of peptides compared with proteins and higher sensitivity than the (non-gel) top-down methods.[7]
Disadvantagesedit
There is limited protein sequence coverage by identified peptides, loss of labile PTMs, and ambiguity of the origin for redundant peptide sequences.[7] Recently the combination of bottom-up and top-down proteomics, so called middle-down proteomics, is receiving a lot of attention as this approach not only can be applied to the analysis of large protein fragments but also avoids redundant peptide sequences.[8]
bottom, proteomics, common, method, identify, proteins, characterize, their, amino, acid, sequences, post, translational, modifications, proteolytic, digestion, proteins, prior, analysis, mass, spectrometry, major, alternative, workflow, used, proteomics, call. Bottom up proteomics is a common method to identify proteins and characterize their amino acid sequences and post translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry 1 2 The major alternative workflow used in proteomics is called top down proteomics where intact proteins are purified prior to digestion and or fragmentation either within the mass spectrometer or by 2D electrophoresis 3 Essentially bottom up proteomics is a relatively simple and reliable means of determining the protein make up of a given sample of cells tissues etc 4 Top down vs bottom up proteomics In bottom up proteomics the crude protein extract is enzymatically digested followed by one or more dimensions of separation of the peptides by liquid chromatography coupled to mass spectrometry a technique known as shotgun proteomics 5 6 By comparing the masses of the proteolytic peptides or their tandem mass spectra with those predicted from a sequence database or annotated peptide spectral in a peptide spectral library peptides can be identified and multiple peptide identifications assembled into a protein identification Contents 1 Advantages 2 Disadvantages 3 See also 4 ReferencesAdvantages editFor high throughput bottom up methods there is better front end separation of peptides compared with proteins and higher sensitivity than the non gel top down methods 7 Disadvantages editThere is limited protein sequence coverage by identified peptides loss of labile PTMs and ambiguity of the origin for redundant peptide sequences 7 Recently the combination of bottom up and top down proteomics so called middle down proteomics is receiving a lot of attention as this approach not only can be applied to the analysis of large protein fragments but also avoids redundant peptide sequences 8 See also editProtein mass spectrometry Shotgun proteomics Peptide mass fingerprinting Top down proteomicsReferences edit Aebersold R Mann M March 2003 Mass spectrometry based proteomics Nature 422 6928 198 207 Bibcode 2003Natur 422 198A doi 10 1038 nature01511 PMID 12634793 Chait BT 2006 Chemistry Mass spectrometry bottom up or top down Science 314 5796 65 6 doi 10 1126 science 1133987 PMID 17023639 Wright EP Partridge MA Padula MP Gauci VJ Malladi CS Coorsen JR 2014 Top down proteomics Enhancing 2D gel electrophoresis from tissue processing to high sensitivity protein detection Proteomics 14 7 8 872 889 doi 10 1002 pmic 201300424 PMID 24452924 Bottom up Proteomics PlanetOrbitrap Thermo Fisher Scientific Retrieved 20 November 2017 Washburn MP Wolters D Yates JR 2001 Large scale analysis of the yeast proteome by multidimensional protein identification technology Nat Biotechnol 19 3 242 247 doi 10 1038 85686 PMID 11231557 Wolters DA Washburn MP Yates JR 2001 An automated multidimensional protein identification technology for shotgun proteomics Anal Chem 73 23 5683 5690 doi 10 1021 ac010617e PMID 11774908 a b Yates JR Ruse CI Nakorchevsky A 2009 Proteomics by Mass Spectrometry Approaches Advances and Applications PDF Annu Rev Biomed Eng 11 49 79 doi 10 1146 annurev bioeng 061008 124934 PMID 19400705 Zhang Yaoyang Fonslow Bryan R Shan Bing Baek Moon Chang Yates John R 2014 04 10 Protein analysis by shotgun bottom up proteomics Chem Rev 113 4 2343 doi 10 1021 cr3003533 PMC 3751594 PMID 23438204 nbsp nbsp This bioinformatics related article is a stub You can help Wikipedia by expanding it vte Retrieved from https en wikipedia org w index php title Bottom up proteomics amp oldid 1184080263, wikipedia, wiki, book, books, library,
