The path to identifying proteins<\/h2>\n\n\n\n![\"Matthias](\"https:\/\/news.embl.de\/wp-content\/uploads\/2017\/12\/171214-mann-219x300.jpg\")
<\/a>Matthias Mann was a group leader at EMBL in Heidelberg (1992-1998). PHOTO: EMBL<\/figcaption><\/figure><\/div>\n\n\n\nMass spectrometry (MS) enables researchers to identify molecules such as proteins and nucleic acids quickly and accurately. Yet while the technique has been used by physicists for the past century, it was not until the 1990s that biologists began to make use of its potential. One of the people driving this biological revolution was EMBL alumnus Matthias Mann, a physicist who led the development of methods that helped bring MS from the margins to the mainstream.<\/p>\n\n\n\n
\u201cAt the time, not many biologists considered using this technology in their research. And even if they did, they never thought it could actually work,\u201d Mann recalls.<\/p>\n\n\n\n
Mass spectrometry, a technique for sorting unknown molecules by their mass and electric charge in order to identify them, requires the molecules to be both electrically charged and in the form of a gas. In order to get them into this state, Mann\u2019s former advisor John Fenn, developed a technology called electrospray ionisation, a method for producing charged particles, for which Fenn was awarded the Nobel Prize<\/a>. Mann then took his advisor\u2019s method one crucial step forward.<\/p>\n\n\n\nElectrospray ionisation requires a quantity of sample that, in the case of samples containing proteins and amino acids, often isn\u2019t available. Along with his group, Mann found that by decreasing the size of the tip through which the solution is sprayed and lowering the rate of the liquid flow through the needle, this new technique, called nanoelectrospray, could be used even on biological samples in tiny quantities.<\/p>\n\n\n\n
Still, nanoelectrospray had its limitations\u2014it could only be used to identify peptides with different masses. (Peptides, like proteins, are compounds composed of amino acids arranged in a set order.) To distinguish peptides of the same mass, he and his team developed yet another technique. They found that peptides could be identified by determining only a tiny stretch\u2014a few amino acids long\u2014plus the masses of the surrounding amino acids. This characteristic chunk provided researchers with a unique fingerprint for the peptide, which they could then compare in a database to determine the identity of the peptide.<\/p>\n\n\n\n
Mann\u2019s postdoctoral student, Andrej Shevchenko<\/a>, further improved sensitivity of identifying peptides by developing a technique to prepare samples containing proteins for nanoelectrospray. By staining the proteins using silver rather than the standard dye, the proteins of interest could be distinguished to a greater degree of sensitivity from the wash of background proteins in the sample.<\/p>\n\n\n\nThese three achievements have made possible his and other teams\u2019 identification of key proteins, which are key contributions to the field of proteomics, the mapping of all proteins in a particular organism. Recently, Mann, who currently works at the University of Copenhagen Denmark<\/a> and at the Max Planck Institute (MPI) of Biochemistry<\/a>, contributed mass spectrometry measurements to a study in which his team identified the almost 11,000 proteins contained in a healthy human heart.<\/p>\n\n\n\nWe knew that this was a start for using mass spectrometry in biology.<\/p><\/blockquote>\n\n\n\n
As Mann looks ahead to identifying proteins in other human organs, his early work at EMBL continues to resonate with him.<\/p>\n\n\n\n
\u201cWhen we were able to find proteins even in minute samples, we knew that this was a start for using mass spectrometry in biology,\u201d Mann recalls. \u201cThat was the best time.\u201d<\/p>\n\n\n\n
Fish development unmasked<\/h2>\n\n\n\n![\"Philipp](\"https:\/\/news.embl.de\/wp-content\/uploads\/2017\/12\/171214-keller-219x300.jpg\")
<\/a>Philipp Keller was a PhD student at EMBL in Heidelberg (2005-2010). PHOTO: EMBL<\/figcaption><\/figure><\/div>\n\n\n\nPhilipp Keller\u2019s fascination with animal development dates back to his training as a physicist. \u201cI enjoy understanding how complex systems work,\u201d he says. \u201cSome of the most complex things, you will find in biology \u2013 like a developing embryo or a higher functioning brain.\u201d After studying physics and computer science at the University of Heidelberg<\/a>, he went on to complete his PhD at EMBL. Not only did he have the opportunity to combine physics and biology studies during his PhD, but he also was able to work in three different labs and with three different advisors \u2013 an interdisciplinary experience that helped direct and shape his research.<\/p>\n\n\n\nFirst Keller worked in Joachim Wittbrodt<\/a>\u2019s group on a project focused on visualising and reconstructing how a zebrafish forms from a single cell. They wanted to know how the single cell divides, migrates and develops into other tissues to form an embryo. It had never been seen before and it was technically difficult to study a vertebrate embryo at the cellular level. \u201cIt was a technology problem,\u201d Keller explains, \u201cso it was natural to form a collaboration with a group that was looking into new tools. I think EMBL is set up to encourage that.\u201d<\/p>\n\n\n\nKeller then began work in Ernst Stelzer<\/a>\u2019s lab on a new kind of microscope, which he called the Digital Scanned Laser Light-Sheet Microscope (DSLM). While the group awaited some parts Keller needed in order to build the new microscope, Keller joined a third project headed by group leader Michael Knop<\/a>: spore formation in yeast. \u201cFrom a modelling perspective, it was interesting to me,\u201d Keller says. \u201cWe wanted to understand this process through computer simulation in addition to experiments.\u201d<\/p>\n\n\n\nI could see the developing fish right in front of my eyes!<\/p><\/blockquote>\n\n\n\n
Once the parts to create the DSLM in Stelzer\u2019s lab arrived, Keller found that the skills he\u2019d learned in computational modelling came full circle in the zebrafish project. The DSLM was faster and produced higher quality images than existing microscopes, which made it possible to image a developing zebrafish embryo for the first time.<\/p>\n\n\n\n
\u201cRather than trying to work through a bunch of text and numbers, I could see the system \u2013 the developing fish \u2013 right in front of my eyes!\u201d, Keller says. This gave him better insight into how biologists think about development at the cellular level.<\/p>\n\n\n\n
<\/a>Mass spectrometry (MS) enables researchers to identify molecules such as proteins and nucleic acids quickly and accurately. Yet while the technique has been used by physicists for the past century, it was not until the 1990s that biologists began to make use of its potential. One of the people driving this biological revolution was EMBL alumnus Matthias Mann, a physicist who led the development of methods that helped bring MS from the margins to the mainstream.<\/p>\n\n\n\n
\u201cAt the time, not many biologists considered using this technology in their research. And even if they did, they never thought it could actually work,\u201d Mann recalls.<\/p>\n\n\n\n
Mass spectrometry, a technique for sorting unknown molecules by their mass and electric charge in order to identify them, requires the molecules to be both electrically charged and in the form of a gas. In order to get them into this state, Mann\u2019s former advisor John Fenn, developed a technology called electrospray ionisation, a method for producing charged particles, for which Fenn was awarded the Nobel Prize<\/a>. Mann then took his advisor\u2019s method one crucial step forward.<\/p>\n\n\n\n Electrospray ionisation requires a quantity of sample that, in the case of samples containing proteins and amino acids, often isn\u2019t available. Along with his group, Mann found that by decreasing the size of the tip through which the solution is sprayed and lowering the rate of the liquid flow through the needle, this new technique, called nanoelectrospray, could be used even on biological samples in tiny quantities.<\/p>\n\n\n\n Still, nanoelectrospray had its limitations\u2014it could only be used to identify peptides with different masses. (Peptides, like proteins, are compounds composed of amino acids arranged in a set order.) To distinguish peptides of the same mass, he and his team developed yet another technique. They found that peptides could be identified by determining only a tiny stretch\u2014a few amino acids long\u2014plus the masses of the surrounding amino acids. This characteristic chunk provided researchers with a unique fingerprint for the peptide, which they could then compare in a database to determine the identity of the peptide.<\/p>\n\n\n\n Mann\u2019s postdoctoral student, Andrej Shevchenko<\/a>, further improved sensitivity of identifying peptides by developing a technique to prepare samples containing proteins for nanoelectrospray. By staining the proteins using silver rather than the standard dye, the proteins of interest could be distinguished to a greater degree of sensitivity from the wash of background proteins in the sample.<\/p>\n\n\n\n These three achievements have made possible his and other teams\u2019 identification of key proteins, which are key contributions to the field of proteomics, the mapping of all proteins in a particular organism. Recently, Mann, who currently works at the University of Copenhagen Denmark<\/a> and at the Max Planck Institute (MPI) of Biochemistry<\/a>, contributed mass spectrometry measurements to a study in which his team identified the almost 11,000 proteins contained in a healthy human heart.<\/p>\n\n\n\n We knew that this was a start for using mass spectrometry in biology.<\/p><\/blockquote>\n\n\n\n As Mann looks ahead to identifying proteins in other human organs, his early work at EMBL continues to resonate with him.<\/p>\n\n\n\n \u201cWhen we were able to find proteins even in minute samples, we knew that this was a start for using mass spectrometry in biology,\u201d Mann recalls. \u201cThat was the best time.\u201d<\/p>\n\n\n\n Philipp Keller\u2019s fascination with animal development dates back to his training as a physicist. \u201cI enjoy understanding how complex systems work,\u201d he says. \u201cSome of the most complex things, you will find in biology \u2013 like a developing embryo or a higher functioning brain.\u201d After studying physics and computer science at the University of Heidelberg<\/a>, he went on to complete his PhD at EMBL. Not only did he have the opportunity to combine physics and biology studies during his PhD, but he also was able to work in three different labs and with three different advisors \u2013 an interdisciplinary experience that helped direct and shape his research.<\/p>\n\n\n\n First Keller worked in Joachim Wittbrodt<\/a>\u2019s group on a project focused on visualising and reconstructing how a zebrafish forms from a single cell. They wanted to know how the single cell divides, migrates and develops into other tissues to form an embryo. It had never been seen before and it was technically difficult to study a vertebrate embryo at the cellular level. \u201cIt was a technology problem,\u201d Keller explains, \u201cso it was natural to form a collaboration with a group that was looking into new tools. I think EMBL is set up to encourage that.\u201d<\/p>\n\n\n\n Keller then began work in Ernst Stelzer<\/a>\u2019s lab on a new kind of microscope, which he called the Digital Scanned Laser Light-Sheet Microscope (DSLM). While the group awaited some parts Keller needed in order to build the new microscope, Keller joined a third project headed by group leader Michael Knop<\/a>: spore formation in yeast. \u201cFrom a modelling perspective, it was interesting to me,\u201d Keller says. \u201cWe wanted to understand this process through computer simulation in addition to experiments.\u201d<\/p>\n\n\n\n I could see the developing fish right in front of my eyes!<\/p><\/blockquote>\n\n\n\n Once the parts to create the DSLM in Stelzer\u2019s lab arrived, Keller found that the skills he\u2019d learned in computational modelling came full circle in the zebrafish project. The DSLM was faster and produced higher quality images than existing microscopes, which made it possible to image a developing zebrafish embryo for the first time.<\/p>\n\n\n\n \u201cRather than trying to work through a bunch of text and numbers, I could see the system \u2013 the developing fish \u2013 right in front of my eyes!\u201d, Keller says. This gave him better insight into how biologists think about development at the cellular level.<\/p>\n\n\n\nFish development unmasked<\/h2>\n\n\n\n
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