Proteomics beyond trypsin
Peptide‐centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large‐scale charting of protein–protein interaction networks, the quantitative analysis of protein post‐translational modifica...
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| Published in | The FEBS journal Vol. 282; no. 14; pp. 2612 - 2626 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
England
Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies
01.07.2015
Blackwell Publishing Ltd |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1742-464X 1742-4658 1742-4658 |
| DOI | 10.1111/febs.13287 |
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| Abstract | Peptide‐centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large‐scale charting of protein–protein interaction networks, the quantitative analysis of protein post‐translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so‐called bottom‐up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi‐protease protein digestion aim to increase proteome sequence coverage and improve the identification of post‐translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle‐down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics‐appropriate proteases. We describe favorable protease traits with an emphasis on middle‐down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome. |
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| AbstractList | Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome.Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome. Peptide‐centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large‐scale charting of protein–protein interaction networks, the quantitative analysis of protein post‐translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so‐called bottom‐up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi‐protease protein digestion aim to increase proteome sequence coverage and improve the identification of post‐translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle‐down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics‐appropriate proteases. We describe favorable protease traits with an emphasis on middle‐down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome. Peptide‐centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large‐scale charting of protein–protein interaction networks, the quantitative analysis of protein post‐translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so‐called bottom‐up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi‐protease protein digestion aim to increase proteome sequence coverage and improve the identification of post‐translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle‐down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics‐appropriate proteases. We describe favorable protease traits with an emphasis on middle‐down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome. Peptide‐centered shotgun analysis of proteins has been the core technology in mass spectrometry‐based proteomics. However, our view of the proteome remains incomplete and this is partially due to the nearly exclusive usage of trypsin. With an emphasis on middle‐down proteomics, we discuss trypsin's shortcomings and the properties of other proteomics‐appropriate proteases. We present sources for the discovery of new proteases. This article is accompanied by a podcast, listen now. Or listen in iTunes. |
| Author | Tsiatsiani, Liana Heck, Albert J. R |
| Author_xml | – sequence: 1 fullname: Tsiatsiani, Liana – sequence: 2 fullname: Heck, Albert J. R |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25823410$$D View this record in MEDLINE/PubMed |
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| Keywords | middle-down proteomics cleavage specificity proteases digestion bias in quantitative proteomics mass spectrometry protein post-translational modifications shotgun proteomics |
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| SubjectTerms | bias in quantitative proteomics cleavage specificity data collection digestion Humans mass spectrometry Mass Spectrometry - methods middle‐down proteomics Peptide Hydrolases - chemistry Peptide Hydrolases - metabolism peptides post-translational modification proteases protein post‐translational modifications Protein Processing, Post-Translational protein-protein interactions Proteins Proteolysis proteome Proteome - chemistry Proteome - metabolism Proteomics Proteomics - methods quantitative analysis shotgun proteomics trypsin Trypsin - chemistry |
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| Title | Proteomics beyond trypsin |
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