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hSWATH : unlocking SWATH’s full potential for an untargeted histone perspective

(2019) JOURNAL OF PROTEOME RESEARCH. 18(11). p.3840-3849
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Abstract
Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis requires a distinct sample preparation, acquisition, and data analysis workflow when compared to traditional MS-based approaches. To this end, sequential window acquisition of all theoretical fragment ion spectra (SWATH) has great potential, as it allows for untargeted accurate identification and quantification of hPTMs. Here, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). We assess its validity on a technical dataset of time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e., acetylated substrate peptides reduce in intensity. We successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.
Keywords
sequential window acquisition of all theoretical fragment ion spectra (SWATH), data-independent acquisition (DIA), histone, mass spectrometry (MS), post-translational modification (PTM), epigenetics, POSTTRANSLATIONAL MODIFICATIONS, QUANTIFICATION, PROTEOMICS, CODE, PROPIONYLATION, WINDOW

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MLA
De Clerck, Laura, et al. “HSWATH : Unlocking SWATH’s Full Potential for an Untargeted Histone Perspective.” JOURNAL OF PROTEOME RESEARCH, vol. 18, no. 11, 2019, pp. 3840–49.
APA
De Clerck, L., Willems, S., Noberini, R., Restellini, C., Van Puyvelde, B., Daled, S., … Dhaenens, M. (2019). hSWATH : unlocking SWATH’s full potential for an untargeted histone perspective. JOURNAL OF PROTEOME RESEARCH, 18(11), 3840–3849.
Chicago author-date
De Clerck, Laura, Sander Willems, Roberta Noberini, Camilla Restellini, Bart Van Puyvelde, Simon Daled, Tiziana Bonaldi, Dieter Deforce, and Maarten Dhaenens. 2019. “HSWATH : Unlocking SWATH’s Full Potential for an Untargeted Histone Perspective.” JOURNAL OF PROTEOME RESEARCH 18 (11): 3840–49.
Chicago author-date (all authors)
De Clerck, Laura, Sander Willems, Roberta Noberini, Camilla Restellini, Bart Van Puyvelde, Simon Daled, Tiziana Bonaldi, Dieter Deforce, and Maarten Dhaenens. 2019. “HSWATH : Unlocking SWATH’s Full Potential for an Untargeted Histone Perspective.” JOURNAL OF PROTEOME RESEARCH 18 (11): 3840–3849.
Vancouver
1.
De Clerck L, Willems S, Noberini R, Restellini C, Van Puyvelde B, Daled S, et al. hSWATH : unlocking SWATH’s full potential for an untargeted histone perspective. JOURNAL OF PROTEOME RESEARCH. 2019;18(11):3840–9.
IEEE
[1]
L. De Clerck et al., “hSWATH : unlocking SWATH’s full potential for an untargeted histone perspective,” JOURNAL OF PROTEOME RESEARCH, vol. 18, no. 11, pp. 3840–3849, 2019.
@article{8638463,
  abstract     = {Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis requires a distinct sample preparation, acquisition, and data analysis workflow when compared to traditional MS-based approaches. To this end, sequential window acquisition of all theoretical fragment ion spectra (SWATH) has great potential, as it allows for untargeted accurate identification and quantification of hPTMs. Here, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). We assess its validity on a technical dataset of time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e., acetylated substrate peptides reduce in intensity. We successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.},
  author       = {De Clerck, Laura and Willems, Sander and Noberini, Roberta and Restellini, Camilla and Van Puyvelde, Bart and Daled, Simon and Bonaldi, Tiziana and Deforce, Dieter and Dhaenens, Maarten},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keywords     = {sequential window acquisition of all theoretical fragment ion spectra (SWATH),data-independent acquisition (DIA),histone,mass spectrometry (MS),post-translational modification (PTM),epigenetics,POSTTRANSLATIONAL MODIFICATIONS,QUANTIFICATION,PROTEOMICS,CODE,PROPIONYLATION,WINDOW},
  language     = {eng},
  number       = {11},
  pages        = {3840--3849},
  title        = {hSWATH : unlocking SWATH’s full potential for an untargeted histone perspective},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.9b00214},
  volume       = {18},
  year         = {2019},
}

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