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http://hdl.handle.net/1942/32714
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DC Field | Value | Language |
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dc.contributor.author | Lacki, Mateusz K. | - |
dc.contributor.author | VALKENBORG, Dirk | - |
dc.contributor.author | Startek, Michal P. | - |
dc.date.accessioned | 2020-11-27T13:10:45Z | - |
dc.date.available | 2020-11-27T13:10:45Z | - |
dc.date.issued | 2020 | - |
dc.date.submitted | 2020-11-05T11:49:38Z | - |
dc.identifier.citation | ANALYTICAL CHEMISTRY, 92 (14) , p. 9472 -9475 | - |
dc.identifier.uri | http://hdl.handle.net/1942/32714 | - |
dc.description.abstract | High-resolution mass spectrometry becomes increasingly available with its ability to resolve the fine isotopic structure of measured analytes. It allows for high-sensitivity spectral deconvolution, leading to less false-positive identifications. Analytes can be identified by comparing their theoretical isotopic signal with the observed peaks. Necessary calculations are, however, computationally demanding and lead to long processing times. For wheat (trictum oestivum) alone, Uniprot holds more than 142 000 candidate protein sequences. This is doubled upon sequence reversal for identification FDR estimation and further multiplied by performing in silico digestion into peptides. The same peptide might originate from more than one protein, which reduces the overall number of sequences to be calculated. However, it is still huge. IsoSpec2 can perform these calculations fast. Compared to IsoSpec1, the algorithm is simpler, orders of magnitude faster, and offers more flexibility for the developers of algorithms for raw data analysis. It is freely available under a 2-clause BSD license, with bindings for the C++, C, R, and Python programming languages. | - |
dc.description.sponsorship | We thank Dr. Blaz.ej Miasojedow. This work was supported by Deutsche Forschungsgemeinschaft DFG (SFB1292, Z01), Bundesministerium fur Bildung und Forschung BMBF (DIASyM, FKZ: 031L0217A), Polish NCN Grants 2017/26/D/ST6/00304, 2018/29/B/ST6/00681, and partially by Flemish SBO Grant InSPECtor, 120025, IWT. Plots were made with ggplot2,43 Keynote, and Inkscape. | - |
dc.language.iso | en | - |
dc.publisher | AMER CHEMICAL SOC | - |
dc.rights | 2020 American Chemical Society. | - |
dc.subject.other | Ion-Cyclotron Resonance | - |
dc.subject.other | Mass-Spectrometry | - |
dc.subject.other | Isotope Distributions | - |
dc.subject.other | Efficient Calculation | - |
dc.subject.other | Resolution | - |
dc.subject.other | Patterns | - |
dc.subject.other | Protein | - |
dc.subject.other | Brain | - |
dc.subject.other | Tesla | - |
dc.title | IsoSpec2: Ultrafast Fine Structure Calculator | - |
dc.type | Journal Contribution | - |
dc.identifier.epage | 9475 | - |
dc.identifier.issue | 14 | - |
dc.identifier.spage | 9472 | - |
dc.identifier.volume | 92 | - |
local.bibliographicCitation.jcat | A1 | - |
dc.description.notes | Lacki, MK (corresponding author), Johannes Gutenberg Univ Mainz, Inst Immunol, Univ Med Ctr, D-55131 Mainz, Germany.; Startek, MP (corresponding author), Univ Warsaw, Dept Math Informat & Mech, PL-02097 Warsaw, Poland. | - |
dc.description.notes | matlacki@uni.mainz.ed; mist@duch.mimuw.edu.pl | - |
dc.description.other | Lacki, MK (corresponding author), Johannes Gutenberg Univ Mainz, Inst Immunol, Univ Med Ctr, D-55131 Mainz, Germany. Startek, MP (corresponding author), Univ Warsaw, Dept Math Informat & Mech, PL-02097 Warsaw, Poland. matlacki@uni.mainz.ed; mist@duch.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/acs.analchem.0c00959 | - |
dc.identifier.pmid | 32501003 | - |
dc.identifier.isi | WOS:000554986200007 | - |
dc.contributor.orcid | Startek, Michal/0000-0001-5227-3447 | - |
local.provider.type | wosris | - |
local.uhasselt.uhpub | yes | - |
local.description.affiliation | [Lacki, Mateusz K.] Johannes Gutenberg Univ Mainz, Inst Immunol, Univ Med Ctr, D-55131 Mainz, Germany. | - |
local.description.affiliation | [Startek, Michal P.] Univ Warsaw, Dept Math Informat & Mech, PL-02097 Warsaw, Poland. | - |
local.description.affiliation | [Valkenborg, Dirk] Hasselt Univ, Data Sci Inst, BE-3500 Hasselt, Belgium. | - |
local.description.affiliation | [Valkenborg, Dirk] Hasselt Univ, Interuniv Inst Biostat & Stat Bioinformat, BE-3500 Hasselt, Belgium. | - |
local.description.affiliation | [Valkenborg, Dirk] Univ Antwerp, Ctr Prote, B-2000 Antwerp, Belgium. | - |
local.description.affiliation | [Valkenborg, Dirk] Flemish Inst Technol Res VITO, Appl Bio & Mol Syst, B-2400 Mol, Belgium. | - |
item.validation | ecoom 2021 | - |
item.contributor | Lacki, Mateusz K. | - |
item.contributor | VALKENBORG, Dirk | - |
item.contributor | Startek, Michal P. | - |
item.accessRights | Restricted Access | - |
item.fullcitation | Lacki, Mateusz K.; VALKENBORG, Dirk & Startek, Michal P. (2020) IsoSpec2: Ultrafast Fine Structure Calculator. In: ANALYTICAL CHEMISTRY, 92 (14) , p. 9472 -9475. | - |
item.fulltext | With Fulltext | - |
crisitem.journal.issn | 0003-2700 | - |
crisitem.journal.eissn | 1520-6882 | - |
Appears in Collections: | Research publications |
Files in This Item:
File | Description | Size | Format | |
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MatheuszLACKI_2020.pdf Restricted Access | Published version | 1.11 MB | Adobe PDF | View/Open Request a copy |
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