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http://hdl.handle.net/1942/38872
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DC Field | Value | Language |
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dc.contributor.author | Radzinski, Piotr | - |
dc.contributor.author | VALKENBORG, Dirk | - |
dc.contributor.author | Startek, Michal Piotr | - |
dc.contributor.author | Gambin, Anna | - |
dc.date.accessioned | 2022-11-15T15:37:05Z | - |
dc.date.available | 2022-11-15T15:37:05Z | - |
dc.date.issued | 2022 | - |
dc.date.submitted | 2022-11-04T11:02:43Z | - |
dc.identifier.citation | JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 33 (11) , p. 2063 -2069 | - |
dc.identifier.uri | http://hdl.handle.net/1942/38872 | - |
dc.description.abstract | Nowadays, monoisotopic mass is used as an important feature in top-down proteomics. Knowing the exact monoisotopic mass is helpfu l for precise and quick protein identification in large protein databases. Howe v e r , only in spectra of small molecules the monoisotopic peak is visible. For bigger molecules like proteins, it is hidden in noise or undetected at all, and therefore its position has to be predicted. By improving the prediction of the peak, we contribute to a more accurate identification of molecules, which is crucial in fields such as chemistry and medicine. In this work, we present the envemind algorit h m , which is a two-step procedure to predict monoisotopic masses of proteins. The prediction is based on an isotopic envelope. Therefore, envemind is dedicated to spectra where we are able to resolve the one dalton separated isotopic variants. Furthermore, only single-molecule spectra are allowed, that is, spectra that do not req u i r e prior deconvolution. The algorit h m deals with the problem of off-by-one dalton errors, which are common in monoisotopic mass prediction. A novel aspect of this work is a mathematical exploration of the space of molecules, where we equate chemical formulas and their theoretical spectrum. Since the space of molecules consists of all possible chemical formulas, this approach is not limited to known substances only. This makes optimization processes faster and enables to approximate theoretical spectrum for a given experimental one. The algorithm is available as a Python package envemind on our GitHub page https://github.com/PiotrRadzinski/envemind . | - |
dc.description.sponsorship | The work was supported by the Polish National Science Centre Grant Nos. 2018/29/B/ST6/00681 and 2017/26/D/ ST6/00304. | - |
dc.language.iso | en | - |
dc.publisher | AMER CHEMICAL SOC | - |
dc.rights | 2022 The Authors. Published by American Chemical Society | - |
dc.subject.other | monoisotopic mass | - |
dc.subject.other | linear model | - |
dc.title | Envemind: Accurate Monoisotopic Mass Determination Based On Isotopic Envelope | - |
dc.type | Journal Contribution | - |
dc.identifier.epage | 2069 | - |
dc.identifier.issue | 11 | - |
dc.identifier.spage | 2063 | - |
dc.identifier.volume | 33 | - |
local.format.pages | 7 | - |
local.bibliographicCitation.jcat | A1 | - |
dc.description.notes | Radzinski, P (corresponding author), Univ Warsaw, Inst Informat, PL-00927 Warsaw, Poland. | - |
dc.description.notes | pmradzinski@mimuw.edu.pl | - |
local.publisher.place | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | - |
local.type.refereed | Refereed | - |
local.type.specified | Article | - |
dc.identifier.doi | 10.1021/jasms.2c00176 | - |
dc.identifier.pmid | 36223196 | - |
dc.identifier.isi | 000870253600001 | - |
dc.contributor.orcid | Radzinski, Piotr/0000-0001-5107-7487 | - |
local.provider.type | wosris | - |
local.description.affiliation | [Valkenborg, Dirk] Hasselt Univ, Interuniv Inst Biostat & Stat Bioinformat, BE-3500 Hasselt, Belgium. | - |
local.description.affiliation | [Radzinski, Piotr; Startek, Michal Piotr; Gambin, Anna] Univ Warsaw, Inst Informat, PL-00927 Warsaw, Poland. | - |
local.description.affiliation | [Startek, Michal Piotr] Gutenberg Univ Mainz, Univ Med Ctr Johannes, Inst Immunol, D-55131 Mainz, Germany. | - |
local.uhasselt.international | yes | - |
item.validation | ecoom 2023 | - |
item.accessRights | Open Access | - |
item.fullcitation | Radzinski, Piotr; VALKENBORG, Dirk; Startek, Michal Piotr & Gambin, Anna (2022) Envemind: Accurate Monoisotopic Mass Determination Based On Isotopic Envelope. In: JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 33 (11) , p. 2063 -2069. | - |
item.fulltext | With Fulltext | - |
item.contributor | Radzinski, Piotr | - |
item.contributor | VALKENBORG, Dirk | - |
item.contributor | Startek, Michal Piotr | - |
item.contributor | Gambin, Anna | - |
crisitem.journal.issn | 1044-0305 | - |
crisitem.journal.eissn | 1879-1123 | - |
Appears in Collections: | Research publications |
Files in This Item:
File | Description | Size | Format | |
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Envemind_ Accurate Monoisotopic Mass Determination Based On Isotopic Envelope.pdf | Published version | 2.02 MB | Adobe PDF | View/Open |
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