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Winners of CASMI2013: Automated Tools and Challenge Data.

ABSTRACT: CASMI (Critical Assessment of Small Molecule Identification) is a contest in which participants identify the molecular formula and chemical structure of challenging molecules using blind mass spectra as the challenge data. Seven research teams participated in CASMI2013. The winner of CASMI2013 was the team of Andrew Newsome and Dejan Nikolic, the University of Illinois at Chicago, IL, USA. The team identified 15 among 16 challenge molecules by manually interpreting the challenge data and by searching in-house and public mass spectral databases, and chemical substance and literature databases. MAGMa was selected as the best automated tool of CASMI2013. In some challenges, most of the automated tools successfully identified the challenge molecules, independent of the compound class and magnitude of the molecular mass. In these challenge data, all of the isotope peaks and the product ions essential for the identification were observed within the expected mass accuracy. In the other challenges, most of the automated tools failed, or identified solution candidates together with many false-positive candidates. We then analyzed these challenge data based on the quality of the mass spectra, the dissociation mechanisms, and the compound class and elemental composition of the challenge molecules.

SUBMITTER: Nishioka T

PROVIDER: S-EPMC4337369 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Winners of CASMI2013: Automated Tools and Challenge Data.

Nishioka Takaaki T Kasama Takeshi T Kinumi Tomoya T Makabe Hidefumi H Matsuda Fumio F Miura Daisuke D Miyashita Masahiro M Nakamura Takemichi T Tanaka Ken K Yamamoto Atsushi A

Mass spectrometry (Tokyo, Japan) 20140902 Spec Iss 2

CASMI (Critical Assessment of Small Molecule Identification) is a contest in which participants identify the molecular formula and chemical structure of challenging molecules using blind mass spectra as the challenge data. Seven research teams participated in CASMI2013. The winner of CASMI2013 was the team of Andrew Newsome and Dejan Nikolic, the University of Illinois at Chicago, IL, USA. The team identified 15 among 16 challenge molecules by manually interpreting the challenge data and by sear ...[more]

PMID: 26819882

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Project description:Cyanine derivatives, named from the Greek word kyanos meaning dark-blue, were discovered more than 150 years ago and remain one of the most widely used classes of organic dyes with contemporary applications in photography (panchromatic emulsions), information storage (CD-R and DVD-R media) and biochemistry (DNA and protein labeling) fields. Cyanine chromogens consist of a charged ?-conjugated segment containing an odd number of sp(2) carbon atoms with the chain capped at the extremities by two electronegative centers, typically nitrogen or oxygen atoms. Cyanines are characterized by a vanishing bond length alternation indicating nearly equal carbon-carbon bond lengths, as well as a very intense and sharp absorption band presenting a shoulder. This hallmark band undergoes a strong red shift when the chain is extended. This so-called vinyl shift is extremely large (ca. 100 nm for each pair of carbon atoms added in the ?-conjugated path), making cyanines ideal building blocks for the design of devices with near-infrared applications. Numerous cyanines also exhibit emission bands with large quantum yields. These exceptional optical properties explain why both canonical cyanines and the corresponding fluoroborates (e.g., boron-dipyrromethene, BODIPY) remain the focus of an ever-growing body of experimental work. In turn, this popularity has stimulated quantum mechanical investigations aiming, on the one hand, at probing the specific electronic nature of cyanine dyes and, on the other hand, at helping to design new dyes. However, the adiabatic approximation to time-dependent density functional theory, the most widespread ab initio model for electronically excited states, fails to accurately reproduce the absorption spectra of cyanine derivatives: it yields a systematic and large underestimation of the experimental wavelengths irrespective of the details of the computational protocol. In contrast, highly correlated wave function approaches provide accurate transition energies for model systems but are hardly applicable to real-life cyanines and BODIPY. This indicates that setting up a computationally tractable theoretical protocol that provides both robust and accurate optical spectra for cyanine-based dyes is a major challenge that has only been taken up lately. In this Account, we compile the most recent advances in the field by considering both compact streptocyanines and large fluoroborates. For the former, we summarize the key results obtained with a large panel of theoretical approaches, allowing us not only to understand the origin of the cyanine challenge but also to pinpoint the schemes presenting the most promising accuracy/effort ratio. For the latter, we show via selected examples how theoretical models can be used to reproduce simultaneously experimental band shapes and transition energies, thus paving the way to an efficient in silico design of new compounds.

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Winners of CASMI2013: Automated Tools and Challenge Data.

Publications

Winners of CASMI2013: Automated Tools and Challenge Data.

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