Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Development of algorithmic and statistical methods in mass spectrometry

2017/26/D/ST6/00304

Keywords:

mass spectrometry algorithmics statistics isotopic envelopes

Descriptors:

  • ST6_6: Algorithms, parallel, distributed and network algorithms, algorithmic game theory
  • ST6_12: Scientific computing, simulation and modelling tools
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Uniwersytet Warszawski, Wydział Matematyki, Informatyki i Mechaniki

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Michał Startek 

Number of co-investigators in the project: 2

Call: SONATA 13 - announced on 2017-06-14

Amount awarded: 348 500 PLN

Project start date (Y-m-d): 2018-04-20

Project end date (Y-m-d): 2022-10-19

Project duration:: 54 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Equipment purchased [PL]

  1. Komputer przenośny (laptop) (2 szt.) (16 000 PLN)

Information in the final report

  • Publication in academic press/journals (5)
  • Articles in post-conference publications (1)
  1. Masserstein: linear regression of mass spectra by optimal transport
    Authors:
    Michał Aleksander Ciach, Błazej Miasojedow, Grzegorz Skoraczynski, Szymon Majewski, Michał Startek, Dirk Valkenborg, Anna Gambin
    Academic press:
    Rapid Communications in Mass Spectrometry (rok: 2021, tom: e8956, strony: N/A (wydanie elektroniczne)), Wydawca: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/rcm.8956 - link to the publication
  2. IsoSpec2: Ultrafast Fine Structure Calculator
    Authors:
    Mateusz K. Łącki, Dirk Valkenborg, and Michał P. Startek
    Academic press:
    Analytical Chemistry (rok: 2020, tom: 92, strony: 9472-9475), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.analchem.0c00959 - link to the publication
  3. Envemind: Accurate Monoisotopic Mass Determination Based On Isotopic Envelope
    Authors:
    Piotr Radziński, Dirk Valkenborg, Michał Piotr Startek, Anna Gambin
    Academic press:
    Journal of the American Society for Mass Spectrometry (rok: 2022, tom: 33, strony: 2063-2069), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/jasms.2c00176 - link to the publication
  4. masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry
    Authors:
    Mateusz K. Łącki, Frederik Lermyte, Błazej Miasojedow, Michał P. Startek, Frank Sobott, Dirk Valkenborg, Anna Gambin
    Academic press:
    Analytical Chemistry (rok: 2019, tom: 91, strony: 1801-1807), Wydawca: American Chemical Society Publications
    Status:
    Published
    DOI:
    10.1021/acs.analchem.8b01479 - link to the publication
  5. OpenMS 3 expands the frontiers of open-source computational mass spectrometry
    Authors:
    Julianus Pfeuffer , Chris Bielow , Samuel Wein , Kyowon Jeong , Eugen Netz , Axel Walter , Oliver Alka , Lars Nilse , Pasquale Colaianni , Douglas McCloskey , Jihyung Kim , George Rosenberger , Leon Bichmann , Mathias Walzer , Johannes Veit , Bertrand Boudaud , Matthias Bernt , Nikolaos Patikas , Matteo Pilz , Michał Startek , Svetlana Kutuzova , Lukas Heumos , Joshua Charkow , Justin Sing , Ayesha Feroz , Arslan Siraj , Hendrik Weisser , Tjeerd Dijkstra , Yasset Perez-Riverol , Hannes Röst , Oliver Kohlbacher
    Academic press:
    Nature Methods , Wydawca: Nature Portfolio
    Status:
    Submitted
    DOI:
    10.21203/rs.3.rs-3286368/v1 - link to the publication
  1. The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution
    Authors:
    Szymon Majewski, Michał Aleksander Ciach, Michał Startek, Wanda Niemyska, Błażej Miasojedow, Anna Gambin
    Conference:
    Workshop on Algorithms in Bioinformatics (WABI) 2018 (rok: 2018, ), Wydawca: Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik
    Data:
    konferencja 20-24 sierpnia
    Status:
    Published
    DOI:
    link to the publication

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