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http://hdl.handle.net/1942/32714
Title: | IsoSpec2: Ultrafast Fine Structure Calculator | Authors: | Lacki, Mateusz K. VALKENBORG, Dirk Startek, Michal P. |
Issue Date: | 2020 | Publisher: | AMER CHEMICAL SOC | Source: | ANALYTICAL CHEMISTRY, 92 (14) , p. 9472 -9475 | 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. | 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. matlacki@uni.mainz.ed; mist@duch.mimuw.edu.pl |
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 | Keywords: | Ion-Cyclotron Resonance;Mass-Spectrometry;Isotope Distributions;Efficient Calculation;Resolution;Patterns;Protein;Brain;Tesla | Document URI: | http://hdl.handle.net/1942/32714 | ISSN: | 0003-2700 | e-ISSN: | 1520-6882 | DOI: | 10.1021/acs.analchem.0c00959 | ISI #: | WOS:000554986200007 | Rights: | 2020 American Chemical Society. | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2021 |
Appears in Collections: | Research publications |
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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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