“Bottom-up proteomics”的意思、由来-开放百科全书

The major alternative workflow used in high-throughput proteomics is called top-down proteomics and does not use proteolytic digestion. Essentially, bottom-up proteomics is a means of determining the protein make-up of a given sample of cells, tissues, etc.^[3]

In bottom-up proteomics, the proteins may first be purified by a method such as gel electrophoresis resulting in one or a few proteins in each proteolytic digest. Alternatively, the crude protein extract is digested directly, followed by one or more dimensions of separation of the peptides by liquid chromatography coupled to mass spectrometry, a technique known as shotgun proteomics.^[4]^[5] 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.

Advantages

There is better front-end separation of peptides compared with proteins and higher sensitivity than the top-down method.^[6]

Disadvantages

There is limited protein sequence coverage by identified peptides, loss of labile PTMs, and ambiguity of the origin for redundant

peptide sequences.^[6] 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.^[7]

See also

References

1. ^{{cite journal |vauthors=Aebersold R, Mann M |title=Mass spectrometry-based proteomics |journal=Nature |volume=422 |issue=6928 |pages=198–207 |date=March 2003 |pmid=12634793 |doi=10.1038/nature01511 |url=|bibcode=2003Natur.422..198A }}
2. ^{{cite journal |author=Chait BT |title=Chemistry. Mass spectrometry: bottom-up or top-down? |journal=Science |volume=314 |issue=5796 |pages=65–6 |year=2006 |pmid=17023639 |doi=10.1126/science.1133987}}
3. ^{{cite web|title=Bottom-up Proteomics|url=http://planetorbitrap.com/bottom-up-proteomics#.WhOjfNjJCUk|website=PlanetOrbitrap|publisher=Thermo Fisher Scientific|accessdate=20 November 2017}}
4. ^{{cite journal |vauthors=Washburn MP, Wolters D, Yates JR |title=Large-scale analysis of the yeast proteome by multidimensional protein identification technology |journal=Nat. Biotechnol. |volume=19 |issue=3 |pages=242–247 |year=2001 |pmid=11231557 |doi=10.1038/85686 }}
5. ^{{cite journal |vauthors=Wolters DA, Washburn MP, Yates JR |title=An automated multidimensional protein identification technology for shotgun proteomics |journal=Anal. Chem. |volume=73 |issue=23 |pages=5683–5690 |year=2001 |pmid=11774908 |doi=10.1021/ac010617e }}
6. ^¹{{cite journal |vauthors=Yates JR, Ruse CI, Nakorchevsky A |title=Proteomics by Mass Spectrometry: Approaches, Advances, and Applications |journal=Annu. Rev. Biomed. Eng. |year=2009 |volume=11 |pages=49–79 |doi=10.1146/annurev-bioeng-061008-124934 |url=http://download.bioon.com.cn/view/upload/month_0910/20091014_179880bfc9f5eeb2548cnpX5P835Y2Cb.attach.pdf |pmid=19400705}}
7. ^{{cite journal|last1=Zhang|first1=Yaoyang|last2=Fonslow|first2=Bryan R.|last3=Shan|first3=Bing|last4=Baek|first4=Moon-Chang|last5=Yates|first5=John R. |title=Protein analysis by shotgun/bottom-up proteomics|journal=Chem Rev|date=2014-04-10|volume=113|issue=4|page=2343|doi=10.1021/cr3003533|pmid=23438204|pmc=3751594}}