Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct
Traditional methods for analysis of peptides using liquid chromatography and tandem mass spectrometry (LC-MS/MS) lack the specificity to comprehensively monitor specific biological processes due to the inherent duty cycle limitations of the MS instrument and the stochastic nature of the analytical p...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2012-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | http://www.mdpi.com/1422-0067/14/1/286 |
| _version_ | 1811211579266433024 |
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| author | Roberto D. Polakiewicz Kimberly A. Lee Xiaoying Jia Jeffrey C. Silva Matthew P. Stokes Michael J. Comb |
| author_facet | Roberto D. Polakiewicz Kimberly A. Lee Xiaoying Jia Jeffrey C. Silva Matthew P. Stokes Michael J. Comb |
| author_sort | Roberto D. Polakiewicz |
| collection | DOAJ |
| description | Traditional methods for analysis of peptides using liquid chromatography and tandem mass spectrometry (LC-MS/MS) lack the specificity to comprehensively monitor specific biological processes due to the inherent duty cycle limitations of the MS instrument and the stochastic nature of the analytical platform. PTMScan Direct is a novel, antibody-based method that allows quantitative LC-MS/MS profiling of specific peptides from proteins that reside in the same signaling pathway. New PTMScan Direct reagents have been produced that target peptides from proteins involved in DNA Damage/Cell Cycle and Apoptosis/Autophagy pathways. Together, the reagents provide access to 438 sites on 237 proteins in these signaling cascades. These reagents have been used to profile the response to UV damage of DNA in human cell lines. UV damage was shown to activate canonical DNA damage response pathways through ATM/ATR-dependent signaling, stress response pathways and induce the initiation of apoptosis, as assessed by an increase in the abundance of peptides corresponding to cleaved, activated caspases. These data demonstrate the utility of PTMScan Direct as a multiplexed assay for profiling specific cellular responses to various stimuli, such as UV damage of DNA. |
| first_indexed | 2024-04-12T05:15:08Z |
| format | Article |
| id | doaj.art-b7348387994348ef87abf14f175f42a0 |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-12T05:15:08Z |
| publishDate | 2012-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-b7348387994348ef87abf14f175f42a02022-12-22T03:46:38ZengMDPI AGInternational Journal of Molecular Sciences1422-00672012-12-0114128630710.3390/ijms14010286Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan DirectRoberto D. PolakiewiczKimberly A. LeeXiaoying JiaJeffrey C. SilvaMatthew P. StokesMichael J. CombTraditional methods for analysis of peptides using liquid chromatography and tandem mass spectrometry (LC-MS/MS) lack the specificity to comprehensively monitor specific biological processes due to the inherent duty cycle limitations of the MS instrument and the stochastic nature of the analytical platform. PTMScan Direct is a novel, antibody-based method that allows quantitative LC-MS/MS profiling of specific peptides from proteins that reside in the same signaling pathway. New PTMScan Direct reagents have been produced that target peptides from proteins involved in DNA Damage/Cell Cycle and Apoptosis/Autophagy pathways. Together, the reagents provide access to 438 sites on 237 proteins in these signaling cascades. These reagents have been used to profile the response to UV damage of DNA in human cell lines. UV damage was shown to activate canonical DNA damage response pathways through ATM/ATR-dependent signaling, stress response pathways and induce the initiation of apoptosis, as assessed by an increase in the abundance of peptides corresponding to cleaved, activated caspases. These data demonstrate the utility of PTMScan Direct as a multiplexed assay for profiling specific cellular responses to various stimuli, such as UV damage of DNA.http://www.mdpi.com/1422-0067/14/1/286proteomicsliquid chromatography tandem mass spectrometryDNA damage responseapoptosispost-translational modificationPTMScan direct |
| spellingShingle | Roberto D. Polakiewicz Kimberly A. Lee Xiaoying Jia Jeffrey C. Silva Matthew P. Stokes Michael J. Comb Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct International Journal of Molecular Sciences proteomics liquid chromatography tandem mass spectrometry DNA damage response apoptosis post-translational modification PTMScan direct |
| title | Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct |
| title_full | Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct |
| title_fullStr | Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct |
| title_full_unstemmed | Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct |
| title_short | Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct |
| title_sort | quantitative profiling of dna damage and apoptotic pathways in uv damaged cells using ptmscan direct |
| topic | proteomics liquid chromatography tandem mass spectrometry DNA damage response apoptosis post-translational modification PTMScan direct |
| url | http://www.mdpi.com/1422-0067/14/1/286 |
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