Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S
Authors
Vizovisek, MatejVidmar, Robert
Van, Quickelberghe Emmy
Impens, Francis
Anđelković, Uroš

Sobotic, Barbara
Stoka, Veronika
Gevaert, Kris
Turk, Boris
Fonovic, Marko
Article (Accepted Version)
Metadata
Show full item recordAbstract
Proteases are important effectors of numerous physiological and pathological processes. Reliable determination of a protease's specificity is crucial to understand protease function and to develop activity-based probes and inhibitors. During the last decade, various proteomic approaches for profiling protease substrate specificities were reported. Although most of these approaches can identify up to thousands of substrate cleavage events in a single experiment, they are often time consuming and methodologically challenging as some of these approaches require rather complex sample preparation procedures. For such reasons their application is often limited to those labs that initially introduced them. Here, we report on a fast and simple approach for proteomic profiling of protease specificities (fast profiling of protease specificity (FPPS)), which can be applied to complex protein mixtures. FPPS is based on trideutero-acetylation of novel N-termini generated by the action of proteases ...and subsequent peptide fractionation on Stage Tips containing ion-exchange and reverse phase chromatographic resins. FPPS can be performed in 2 days and does not require extensive fractionation steps. Using this approach, we have determined the specificity profiles of the cysteine cathepsins K, L and S. We further validated our method by comparing the results with the specificity profiles obtained by the N-terminal combined fractional diagonal chromatography method. This comparison pointed to almost identical substrate specificities for all three cathepsins and confirmed the reliability of the FPPS approach. All MS data have been deposited in the ProteomeXchange with identifiers PXD001536 and PXD001553 (; ).
Keywords:
Cathepsin protease specificity / Intact protein-based cleavage site discovery / N-terminomics / TechnologySource:
Proteomics, 2015, 15, 14, 2479-2490Publisher:
- Wiley-Blackwell, Hoboken
Funding / projects:
- Slovenian Research Agency - P1-0140
- Slovenian Research Agency - J1-3602
- Slovenian Research Agency - N1-0022
- Slovenian Research Agency - J1-0185
- Research Foundation - Flanders (FWO-Vlaanderen) - G.0048.08
- Research Foundation - Flanders (FWO-Vlaanderen) - G.0C37.14N
Note:
- This is peer-reviewed version of the artcle: M. Vizovišek, R. Vidmar, E. Van Quickelberghe, F. Impens, U. Andjelković, B. Sobotič, V. Stoka, K. Gevaert, B. Turk, M. Fonović, Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S, Proteomics. 15 (2015) 2479–2490. https://doi.org/10.1002/pmic.201400460
- Published version: http://cer.ihtm.bg.ac.rs/handle/123456789/1626
DOI: 10.1002/pmic.201400460
ISSN: 1615-9853
PubMed: 25626674
WoS: 000357946600011
Scopus: 2-s2.0-84924390096
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IHTMTY - JOUR AU - Vizovisek, Matej AU - Vidmar, Robert AU - Van, Quickelberghe Emmy AU - Impens, Francis AU - Anđelković, Uroš AU - Sobotic, Barbara AU - Stoka, Veronika AU - Gevaert, Kris AU - Turk, Boris AU - Fonovic, Marko PY - 2015 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/3209 AB - Proteases are important effectors of numerous physiological and pathological processes. Reliable determination of a protease's specificity is crucial to understand protease function and to develop activity-based probes and inhibitors. During the last decade, various proteomic approaches for profiling protease substrate specificities were reported. Although most of these approaches can identify up to thousands of substrate cleavage events in a single experiment, they are often time consuming and methodologically challenging as some of these approaches require rather complex sample preparation procedures. For such reasons their application is often limited to those labs that initially introduced them. Here, we report on a fast and simple approach for proteomic profiling of protease specificities (fast profiling of protease specificity (FPPS)), which can be applied to complex protein mixtures. FPPS is based on trideutero-acetylation of novel N-termini generated by the action of proteases and subsequent peptide fractionation on Stage Tips containing ion-exchange and reverse phase chromatographic resins. FPPS can be performed in 2 days and does not require extensive fractionation steps. Using this approach, we have determined the specificity profiles of the cysteine cathepsins K, L and S. We further validated our method by comparing the results with the specificity profiles obtained by the N-terminal combined fractional diagonal chromatography method. This comparison pointed to almost identical substrate specificities for all three cathepsins and confirmed the reliability of the FPPS approach. All MS data have been deposited in the ProteomeXchange with identifiers PXD001536 and PXD001553 (; ). PB - Wiley-Blackwell, Hoboken T2 - Proteomics T1 - Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S VL - 15 IS - 14 SP - 2479 EP - 2490 DO - 10.1002/pmic.201400460 ER -
@article{ author = "Vizovisek, Matej and Vidmar, Robert and Van, Quickelberghe Emmy and Impens, Francis and Anđelković, Uroš and Sobotic, Barbara and Stoka, Veronika and Gevaert, Kris and Turk, Boris and Fonovic, Marko", year = "2015", abstract = "Proteases are important effectors of numerous physiological and pathological processes. Reliable determination of a protease's specificity is crucial to understand protease function and to develop activity-based probes and inhibitors. During the last decade, various proteomic approaches for profiling protease substrate specificities were reported. Although most of these approaches can identify up to thousands of substrate cleavage events in a single experiment, they are often time consuming and methodologically challenging as some of these approaches require rather complex sample preparation procedures. For such reasons their application is often limited to those labs that initially introduced them. Here, we report on a fast and simple approach for proteomic profiling of protease specificities (fast profiling of protease specificity (FPPS)), which can be applied to complex protein mixtures. FPPS is based on trideutero-acetylation of novel N-termini generated by the action of proteases and subsequent peptide fractionation on Stage Tips containing ion-exchange and reverse phase chromatographic resins. FPPS can be performed in 2 days and does not require extensive fractionation steps. Using this approach, we have determined the specificity profiles of the cysteine cathepsins K, L and S. We further validated our method by comparing the results with the specificity profiles obtained by the N-terminal combined fractional diagonal chromatography method. This comparison pointed to almost identical substrate specificities for all three cathepsins and confirmed the reliability of the FPPS approach. All MS data have been deposited in the ProteomeXchange with identifiers PXD001536 and PXD001553 (; ).", publisher = "Wiley-Blackwell, Hoboken", journal = "Proteomics", title = "Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S", volume = "15", number = "14", pages = "2479-2490", doi = "10.1002/pmic.201400460" }
Vizovisek, M., Vidmar, R., Van, Q. E., Impens, F., Anđelković, U., Sobotic, B., Stoka, V., Gevaert, K., Turk, B.,& Fonovic, M.. (2015). Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S. in Proteomics Wiley-Blackwell, Hoboken., 15(14), 2479-2490. https://doi.org/10.1002/pmic.201400460
Vizovisek M, Vidmar R, Van QE, Impens F, Anđelković U, Sobotic B, Stoka V, Gevaert K, Turk B, Fonovic M. Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S. in Proteomics. 2015;15(14):2479-2490. doi:10.1002/pmic.201400460 .
Vizovisek, Matej, Vidmar, Robert, Van, Quickelberghe Emmy, Impens, Francis, Anđelković, Uroš, Sobotic, Barbara, Stoka, Veronika, Gevaert, Kris, Turk, Boris, Fonovic, Marko, "Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S" in Proteomics, 15, no. 14 (2015):2479-2490, https://doi.org/10.1002/pmic.201400460 . .