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Proteomics Master John Yates:a fan of mass spectrometry

Reviewing the centennial development history of mass spectrometry, thanks to the continuous innovation of machinery, electronics and computer industries, the performance of mass spectrometer is also improving. What really promotes the leap of mass spectrometry is those accidentalrevolutionary innovation ,即具有颠覆性的技术创新——创造全新的分析规模和能力水平。蛋白质组学的大规模分析亦是revolutionary innovation 所推动实现的,John Yates III便是实现这项工作的关键科学家之一。

John Yates:I was instantly hooked when I first saw a mass spectrometer.  

Infatuation and mass spectrometry

As the inventor of MudPIT (multi-dimensional protein identification technology) and sequence, John Yates has brought a breakthrough in proteomics technology, and his every achievement is inseparable from his love for mass spectrometry.

Yates also said frankly in an interview that he was killed when he first saw the mass spectrum“Instantly hooked”

John Yates, inventor of MudPIT and sequence

According to Yates, he was an undergraduate at that time. At the moment when he saw how the mass spectrometer worked, he exclaimed,”it’s so cool!”; When he saw the full computers in the laboratory, he was shocked by its powerful data processing ability.

Therefore, Yates, who received a bachelor’s degree in zoology from the University of Maine in 1980, chose to continue his postgraduate course in chemistry at the University. In the course of study, in order to further explore the relationship between mass spectrometry and proteomic research, the doer Yates contacted don hunt of the University of Virginia (Professor of chemistry and pathology department of the University of Virginia). Soon after, he received a handwritten invitation and began his research at the University of Virginia.

At the same time, Yates has seen the potential of mass spectrometry and hopes to apply it to proteomic research, but it is limited by”unable to quickly analyze the data manually”. Therefore, he led his team to develop the software tool sequence, a translator of mass spectrometry data, in 1994.

John Yates invented sequence algorithm

Release the charm of mass spectrometry |”translator” sequence

To some extent, the development of sequence is inevitable.

In 1990, the United States Department of energy and the National Institutes of health submitted a joint plan for human genome sequencing to the United States Congress. Since then, the database began to be full of DNA sequence information, and a large number of relevant algorithms for data mining bioinformatics have emerged.

1994 was the first year of the birth of data dependent acquisition (DDA), and the groundbreaking achievement sequence was also born in this year, attracting worldwide attention.

As the founder of bottom-up proteomics (bottom-up method:analyzing peptides after enzymatic hydrolysis of proteins), the creation of sequence not only laid the core foundation of proteomics research, made more researchers in the field of life sciences realize and recognize the value of proteomics, but also showed the charm and potential of mass spectrometry to the world.

In short, sequence interprets the information of mass spectrometry (i.e. peptides and proteins) by using the information of human genomics. When studying proteins in cells, thanks to this method, researchers do not need to purify each protein. They only need to cut the whole protein, and then analyze each protein by mass spectrometry to obtain the information of all proteins.

The sequence analysis method can be divided into four steps:(1) compress the mass spectrometry data; (2) By comparing the information of protein database and experimental mass spectrometry data at the molecular weight level, the possible polypeptide sequences are matched; (3) The predicted fragment ions of the sequences obtained from the database are compared with the mass spectrometry information to generate the best matching sequence table; This sequence is used for scoring and statistical operations, and then (4) get the analysis results.

Sequence analysis steps

This method not only adopts the most cutting-edge technology at that time, such as fast Fourier transform (FFT) for cross-correlation, but also integrates the author’s bold assumptions after in-depth understanding of mass spectrometry data, such as systematic normalization of data and multiple empirical scoring weights.

Sequence improves the effectiveness and accuracy of mass spectrometry technology and can solve key biological and clinical problems. Since its development, researchers all over the world have studied most proteins in organelles and”painted” them according to the difference of protein expression between normal and disease states, so as to reveal the mechanism of disease occurrence and development.

In addition, this work has also promoted the large-scale application of proteomics (which will be introduced below), which he himself applied to the large-scale study of determining the composition of protein complexes in single-cell organisms and mammalian cells. A series of other software were also developed under the influence of sequence, which promoted the various applications of proteome in molecular and cell biology research, including qualitative and quantitative analysis of peptides/proteins, identification of post-translational modifications, dynamic study of protein structure and so on.

New battlefield | large scale identification of proteins

In 1998, Yates proposed shotgun proteomics to promote large-scale identification and analysis of proteome. This idea comes from Celera Genomics, one of the producers of the draft human genome. They adopted a very advanced gene sequencing technology at that time:shotgun method. This method skips the process of splitting and cloning the genome and directly breaks it into small fragments for random sequencing, just like a jigsaw puzzle:we buy a complete jigsaw puzzle home, completely disrupt it, and then start the game journey.

In 2001, based on the idea of shotgun proteomics, John Yates team developed MudPIT technology and published its results in Nature Biotechnology. The article is entitled large-scale analysis of the year protein by multidimensional protein identification technology. The application of shotgun method to proteomics is a milestone development achievement. It not only subverts the traditional protein analysis methods, but also promotes the realization of large-scale analysis.

Yates led the team to develop MudPIT

At that time, the most widely used method for protein analysis and identification was two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). This technology identified proteins through the two dimensions of isoelectric point (PI) and molecular weight (MW). It has the characteristics of high resolution.

However, 2D-PAGE has some insurmountable defects:(1) although this technology can provide information such as relative molecular weight, isoelectric point and relative amount of expression abundance, it can not complete some more”fine” tasks, such as the detection of low abundance protein points, the separation of proteins in extremely acidic and alkaline regions and proteins in high molecular weight regions; On the other hand, (2) this technology has low degree of automation, poor repeatability and long time-consuming; In addition, (3) identification quantity and flux have always been the bottleneck of this technology.

In contrast, MudPIT is a non gel technology, which can realize the separation and identification of a component in a complex mixture of proteins and peptides. Firstly, the peptides were separated in two-dimensional liquid chromatography, then separated in multi-dimensional capillary liquid chromatography, then analyzed by tandem mass spectrometry and finally searched the database. This technology can quickly analyze proteins with less samples, and is suitable for the separation and identification of large-scale proteins in proteomics.

Yates’ article fully demonstrates the advantages of MudPIT over 2D-PAGE technology. They completed the largest amount of protein identification research at that time:1484 proteins were isolated and identified from the proteome of S. cerevisiae; In contrast, the largest proteomic study based on 2D-PAGE at that time identified only 502 proteins of Haemophilus influenza proteome.

Overall, the sensitivity and dynamic monitoring range of MudPIT have made greater progress, with wider application range and high degree of automation. Therefore, MudPIT has also become a powerful tool for studying large-scale protein expression, qualitative and quantitative in complex biological samples in the first decade of the 20th century.

Winning password | innovation and cooperation

John Yates:I’ve become very intrigued with the concept of innovation.

Scientific research progress depends heavily on the high-intensity tackling and continuous innovation of researchers. They need to constantly”make things difficult” for themselves and others, and maintain the sensitivity of new directions and new ideas. Yates has always hoped that more scientists can continue to innovate in his methods.

In order to help scientists innovate and eliminate their own methods as soon as possible, Yates shared his”Innovation book list” and hoped that everyone could learn the innovation path from the book and get inspiration, such as Jon gertner’s the idea factory (this is a biography about the legendary scientific research institution – Bell laboratory, which gave birth to 9 Nobel Prize winners), And Steven Johnson’s where good ideas come from (in this book, the author goes deep into the natural history of innovation, tracks it across disciplines and fields, and determines seven key modes of innovation).

Yates also recalled that when discussing cooperation with a mass spectrometry manufacturer in 2003, his first question was”can the scanning speed be faster?” It is this problem that makes us welcome the upgraded mass spectrometer. In addition, when the new equipment is ready to land, Yates will continue to put forward new ideas and discuss with partners to find a better solution.

In addition to innovation, Yates also advocates teamwork and has trained more than 70 excellent scientists. Michael Washburn, one of the researchers who once worked as a postdoctoral in Yates Laboratory (currently a professor of tumor biology at the University of Kansas Medical Center), said Yates made him deeply aware of the need to establish a multidisciplinary team. Because mass spectrometry research is not a stand-alone game, it extremely needs interdisciplinary methodology and mutual teaching of compound talents to solve the research bottleneck and achieve results. Therefore, after developing MudPIT with Yates that year, Washburn continued to expand its territory in the field of proteomics and is famous for studying chromatin remodeling complexes based on mass spectrometry.

Michael Washburn

Achievements and roots | young proteomics

The development of sequence and MudPIT and other outstanding scientific research achievements have established Yates’s leading position in the field of proteomics. He was not surprised to be selected into the list of”top 100 chemists in the world from 2000 to 2010″ in 2011.

John Yates was selected into the list of”top 100 chemists in the world from 2000 to 2010″ in 2011

In addition, he won the ASMS mass spectrometry outstanding contribution award and khwarizmi International Award in 2019 to recognize his contribution to proteomics.

Proteomics is only more than 20 years since its birth (1997). Thanks to the unremitting efforts of global scientists and HUPO, this young frontier discipline has achieved many exciting and amazing milestone achievements. We look forward to more young researchers participating in proteomics in the future支点,揭示生命的奥秘,开创疾病治疗的新篇章。

年轻科研力量的崛起是科技创新、发展的重要引擎。2015年,HUPO特设Early Career Researchers (ECRs)项目,以推动年轻科研人员对新知识、新思想和前沿科技创新的引领作用。具体而言,该项目的主旨为:

(1)为ECR提供更多研究和交流平台,提高他们的科学知名度:HUPO设立稿件竞赛 (Manuscript Competition),以便让杰出的年轻科学们展示自己最新工作成果;

(2)为ECR策划职业发展相关活动,提高他们在学术界、工业界的竞争力:HUPO邀请来自不同科研、技术和商业领域的世界知名科学家,分享他们的科研经历与职业生涯;

(3)提高蛋白质组学领域的公平性、多样性和包容性。


参考资料

1. Washburn, M. P., Wolters, D., & Yates, J. R. (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature biotechnology, 19(3), 242-247.

2. Proteomics goes global. Nature biotechnology, 24, 302–303 (2006). https://doi.org/10.1038/nbt0306-302

3. Eng, K. J., McCormack, A. L., & Yates, J. R. (1994). An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society Mass Spectrometry, 5(11), 976–989.

4. Yates, J. R. (2013). The revolution and evolution of shotgun proteomics for large-scale proteome analysis. Journal of the American Chemical Society, 135(5), 1629-1640.

5. Vivien, M. (2013). Digging deep into proteomes. Nature Method, 10(1), 3.

6. MICHGAN STATE UNIVERSITY. (n.d). Dr. Michael Washburn. Retrieved from https://bmb.natsci.msu.edu/about/awards/john-a-boezi-memorial-alumnus-award/dr-michael-washburn/

7. Scripps Research. (2019). Chemist John Yates receives 2019 ASMS John B. Fenn Award for innovations that advanced mass spectrometry. Retrieved from https://www.scripps.edu/news-and-events/press-room/2019/20190614-yates-amsmaward.html