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Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications

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Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications. / Preston, George; Yang, Liping; Phillips, David; Maier, Claudia.

In: PloS one, Vol. 15, No. 7, e0235263, 08.07.2020, p. e0235263.

Research output: Contribution to journalArticle

Harvard

Preston, G, Yang, L, Phillips, D & Maier, C 2020, 'Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications', PloS one, vol. 15, no. 7, e0235263, pp. e0235263. https://doi.org/10.1371/journal.pone.0235263

APA

Preston, G., Yang, L., Phillips, D., & Maier, C. (2020). Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications. PloS one, 15(7), e0235263. [e0235263]. https://doi.org/10.1371/journal.pone.0235263

Vancouver

Preston G, Yang L, Phillips D, Maier C. Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications. PloS one. 2020 Jul 8;15(7):e0235263. e0235263. https://doi.org/10.1371/journal.pone.0235263

Author

Preston, George ; Yang, Liping ; Phillips, David ; Maier, Claudia. / Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications. In: PloS one. 2020 ; Vol. 15, No. 7. pp. e0235263.

Bibtex Download

@article{55d62b00202949a980ff6c4d5638a1c9,
title = "Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications",
abstract = "Dependent peptide searching is a method for discovering covalently-modified peptides – and therefore proteins – in mass-spectrometry-based proteomics experiments. Being more permissive than standard search methods, it has the potential to discover novel modifications (e.g., post-translational modifications occurring in vivo, or modifications introduced in vitro). However, few studies have explored dependent peptide search results in an untargeted way. In the present study, we sought to evaluate dependent peptide searching as a means of characterising proteins that have been modified in vitro. We generated a model data set by analysing N-ethylmaleimide-treated bovine serum albumin, and performed dependent peptide searches using the popular MaxQuant software. To facilitate interpretation of the search results (hundreds of dependent peptides), we developed a series of visualisation tools (R scripts). We used the tools to assess the diversity of putative modifications in the albumin, and to pinpoint hypothesised modifications. We went on to explore the tools{\textquoteright} generality via analyses of public data from studies of rat and human proteomes. Of 19 expected sites of modification (one in rat cofilin-1 and 18 across six different human plasma proteins), eight were found and correctly localised. Apparently, some sites went undetected because chemical enrichment had depleted necessary analytes (potential {\textquoteleft}base{\textquoteright} peptides). Our results demonstrate (i) the ability of the tools to provide accurate and informative visualisations, and (ii) the usefulness of dependent peptide searching for characterising in vitro protein modifications. Our model data are available via PRIDE/ProteomeXchange (accession number PXD013040).",
author = "George Preston and Liping Yang and David Phillips and Claudia Maier",
year = "2020",
month = jul,
day = "8",
doi = "10.1371/journal.pone.0235263",
language = "English",
volume = "15",
pages = "e0235263",
journal = "PloS one",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications

AU - Preston, George

AU - Yang, Liping

AU - Phillips, David

AU - Maier, Claudia

PY - 2020/7/8

Y1 - 2020/7/8

N2 - Dependent peptide searching is a method for discovering covalently-modified peptides – and therefore proteins – in mass-spectrometry-based proteomics experiments. Being more permissive than standard search methods, it has the potential to discover novel modifications (e.g., post-translational modifications occurring in vivo, or modifications introduced in vitro). However, few studies have explored dependent peptide search results in an untargeted way. In the present study, we sought to evaluate dependent peptide searching as a means of characterising proteins that have been modified in vitro. We generated a model data set by analysing N-ethylmaleimide-treated bovine serum albumin, and performed dependent peptide searches using the popular MaxQuant software. To facilitate interpretation of the search results (hundreds of dependent peptides), we developed a series of visualisation tools (R scripts). We used the tools to assess the diversity of putative modifications in the albumin, and to pinpoint hypothesised modifications. We went on to explore the tools’ generality via analyses of public data from studies of rat and human proteomes. Of 19 expected sites of modification (one in rat cofilin-1 and 18 across six different human plasma proteins), eight were found and correctly localised. Apparently, some sites went undetected because chemical enrichment had depleted necessary analytes (potential ‘base’ peptides). Our results demonstrate (i) the ability of the tools to provide accurate and informative visualisations, and (ii) the usefulness of dependent peptide searching for characterising in vitro protein modifications. Our model data are available via PRIDE/ProteomeXchange (accession number PXD013040).

AB - Dependent peptide searching is a method for discovering covalently-modified peptides – and therefore proteins – in mass-spectrometry-based proteomics experiments. Being more permissive than standard search methods, it has the potential to discover novel modifications (e.g., post-translational modifications occurring in vivo, or modifications introduced in vitro). However, few studies have explored dependent peptide search results in an untargeted way. In the present study, we sought to evaluate dependent peptide searching as a means of characterising proteins that have been modified in vitro. We generated a model data set by analysing N-ethylmaleimide-treated bovine serum albumin, and performed dependent peptide searches using the popular MaxQuant software. To facilitate interpretation of the search results (hundreds of dependent peptides), we developed a series of visualisation tools (R scripts). We used the tools to assess the diversity of putative modifications in the albumin, and to pinpoint hypothesised modifications. We went on to explore the tools’ generality via analyses of public data from studies of rat and human proteomes. Of 19 expected sites of modification (one in rat cofilin-1 and 18 across six different human plasma proteins), eight were found and correctly localised. Apparently, some sites went undetected because chemical enrichment had depleted necessary analytes (potential ‘base’ peptides). Our results demonstrate (i) the ability of the tools to provide accurate and informative visualisations, and (ii) the usefulness of dependent peptide searching for characterising in vitro protein modifications. Our model data are available via PRIDE/ProteomeXchange (accession number PXD013040).

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U2 - 10.1371/journal.pone.0235263

DO - 10.1371/journal.pone.0235263

M3 - Article

VL - 15

SP - e0235263

JO - PloS one

JF - PloS one

SN - 1932-6203

IS - 7

M1 - e0235263

ER -

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