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Ciach MA, Miasojedow B, Skoraczyński G, Majewski S, Startek M, Valkenborg D, Gambin A. Masserstein: Linear regression of mass spectra by optimal transport. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020:e8956. [PMID: 32996651 DOI: 10.1002/rcm.8956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/31/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The linear regression of mass spectra is a computational problem defined as fitting a linear combination of reference spectra to an experimental one. It is typically used to estimate the relative quantities of selected ions. In this work, we study this problem in an abstract setting to develop new approaches applicable to a diverse range of experiments. METHODS To overcome the sensitivity of the ordinary least-squares regression to measurement inaccuracies, we base our methods on a non-conventional spectral dissimilarity measure, known as the Wasserstein or the Earth Mover's distance. This distance is based on the notion of the cost of transporting signal between mass spectra, which renders it naturally robust to measurement inaccuracies in the mass domain. RESULTS Using a data set of 200 mass spectra, we show that our approach is capable of estimating ion proportions accurately without extensive preprocessing of spectra required by other methods. The conclusions are further substantiated using data sets simulated in a way that mimics most of the measurement inaccuracies occurring in real experiments. CONCLUSIONS We have developed a linear regression algorithm based on the notion of the cost of transporting signal between spectra. Our implementation is available in a Python 3 package called masserstein, which is freely available at https://github.com/mciach/masserstein.
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Affiliation(s)
- Michał Aleksander Ciach
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
| | - Błażej Miasojedow
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Grzegorz Skoraczyński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Szymon Majewski
- Institute of Mathematics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Startek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Dirk Valkenborg
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
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Font M, Plano D, Sanmartín C, Palop JA. Topological and quantum molecular descriptors as effective tools for analyzing cytotoxic activity achieved by a series of (diselanediyldibenzene-4,1-diylnide)biscarbamate derivatives. J Mol Graph Model 2017; 73:62-73. [PMID: 28236745 DOI: 10.1016/j.jmgm.2017.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/28/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022]
Abstract
A molecular modeling study has been carried out on a previously reported series of (diselanediyldibenzene-4,1-diylnide)biscarbamate derivatives that show cytotoxic and antiproliferative in vitro activity against MCF-7 human cell line; radical scavenging properties were also confirmed when these compounds were tested for their ability to scavenge DPPH and ABTS radicals. The data obtained allowed us to classify the compounds into two different groups: (a) aliphatic carbamates for which the activity could be related with a first nucleophilic attack (mediated by H2O, for example) on the selenium atoms of the central scaffold, followed by the release of the alkyl N-(4-selanylphenyl) and N-(4-selenenophenyl)carbamate moieties. Then, a second nucleophilic attack on the carbamate moiety, to yield 4-aminobenzeneselenol and 4-selenenoaniline respectively, which can ultimately be responsible for the activity of the compounds; (b) aromatic carbamates, for which we propose a preferred nucleophilic attack on the carbamate moiety, yielding 4-[(4-aminophenyl)diselanyl]aniline, the common structural fragment for this series, for which we have previously demonstrated its cytotoxic profile. Then, selenium atoms of the central fragment may later undergo a new nucleophilic attack, to yield 4-selenenoaniline and 4-aminobenzeneselenol. The phenolic moieties released in this process may also have a synergistic cytotoxic and redox activity. The data that support this connection include the conformational behavior and the molecular topography of the derivatives which can influence the accessibility of the hydrolysis points, and some quantum descriptors (bond order, atomic charges, total valences, ionization potential, electron affinity, HOMO 0 and LUMO 0 location, etc.) that have been related to the biological activity of the compounds.
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Affiliation(s)
- María Font
- University of Navarra, School of Pharmacy and Nutrition, Dpto de Química Orgánica y Farmacéutica, Sección de Modelización Molecular, Irunlarrea, 1, Pamplona, E-31008, Spain; IdISNA, Instituto de Investigación Sanitaria de Navarra, Recinto del Complejo Hospitalario de Navarra, Irunlarrea 3, Pamplona, E-31008, Spain.
| | - Daniel Plano
- IdISNA, Instituto de Investigación Sanitaria de Navarra, Recinto del Complejo Hospitalario de Navarra, Irunlarrea 3, Pamplona, E-31008, Spain; University of Navarra, School of Pharmacy and Nutrition, Dpto de Química Orgánica y Farmacéutica, Sección de Síntesis, Navarra, Irunlarrea, 1, Pamplona, E-31008, Spain
| | - Carmen Sanmartín
- IdISNA, Instituto de Investigación Sanitaria de Navarra, Recinto del Complejo Hospitalario de Navarra, Irunlarrea 3, Pamplona, E-31008, Spain; University of Navarra, School of Pharmacy and Nutrition, Dpto de Química Orgánica y Farmacéutica, Sección de Síntesis, Navarra, Irunlarrea, 1, Pamplona, E-31008, Spain
| | - Juan Antonio Palop
- University of Navarra, School of Pharmacy and Nutrition, Dpto de Química Orgánica y Farmacéutica, Sección de Síntesis, Navarra, Irunlarrea, 1, Pamplona, E-31008, Spain
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Geronés M, Rodríguez Pirani LS, Erben MF, Romano RM, Cavasso Filho RL, Tong SR, Ge M, Della Védova CO. Photoelectron Spectroscopy and Ionic Fragmentation of OSeCl 2 and Its Analogue OSCl 2 under VUV Irradiation. J Phys Chem A 2015; 119:8000-9. [DOI: 10.1021/acs.jpca.5b02162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mariana Geronés
- CEQUINOR
(CONICET-UNLP), Departamento de Química, Facultad de Ciencias
Exactas, Universidad Nacional de La Plata, C. C. 962 (1900) La Plata, República Argentina
| | - Lucas S. Rodríguez Pirani
- CEQUINOR
(CONICET-UNLP), Departamento de Química, Facultad de Ciencias
Exactas, Universidad Nacional de La Plata, C. C. 962 (1900) La Plata, República Argentina
| | - Mauricio F. Erben
- CEQUINOR
(CONICET-UNLP), Departamento de Química, Facultad de Ciencias
Exactas, Universidad Nacional de La Plata, C. C. 962 (1900) La Plata, República Argentina
| | - Rosana M. Romano
- CEQUINOR
(CONICET-UNLP), Departamento de Química, Facultad de Ciencias
Exactas, Universidad Nacional de La Plata, C. C. 962 (1900) La Plata, República Argentina
| | | | - Sheng Rui Tong
- State
Key Laboratory for Structural Chemistry of Unstable and Stable Species,
Beijing National Laboratory for Molecular Sciences (BNLMS), Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100080, People’s Republic of China
| | - Maofa Ge
- State
Key Laboratory for Structural Chemistry of Unstable and Stable Species,
Beijing National Laboratory for Molecular Sciences (BNLMS), Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100080, People’s Republic of China
| | - Carlos O. Della Védova
- CEQUINOR
(CONICET-UNLP), Departamento de Química, Facultad de Ciencias
Exactas, Universidad Nacional de La Plata, C. C. 962 (1900) La Plata, República Argentina
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Li H, O'Connor PB. Electron capture dissociation of disulfide, sulfur-selenium, and diselenide bound peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2001-2010. [PMID: 22993041 DOI: 10.1007/s13361-012-0473-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 06/01/2023]
Abstract
To examine the electron capture dissociation (ECD) behavior of disulfide (S-S), sulfur-selenium (S-Se), and diselenide (Se-Se) bonds-containing peptides, a series of free cysteine (Cys) and selenocysteine (Sec) containing peptides were reacted to form interchain S-S, S-Se, and Se-Se bonds, and then studied using ECD with Fourier transform ion cyclotron mass spectrometry (FTICR MS). These results demonstrate that the radical has higher tendency to stay at selenium rather than sulfur after the cleavage of Se-S bonds by ECD. In addition, -SH (-33), -S (-32), and -S + H (-31) small neutral losses were all observed from the cleavage of C-S bonds of a disulfide bound peptide. Similar, but minor, fragments were also detected in S-Se bound peptides. In contrast, the cleavage of C-Se bonds of the Se-Se species mainly forms fragments with neutral loss of -Se + H (-78.90868), and the radical tends to stay on the selenium of its corresponding complementary pair. Although the electron affinities of S atom (2.07 eV) and Se atom (2.02 eV) are very close; they have very different reactivity towards electrons. The replacement of sulfur with selenium greatly increases the electron affinities of S-Se and Se-Se bonds comparing to S-S bonds (with an increase of electron affinity by about 0.20 eV by replacing a sulfur with a selenium) (Int J Quantum Chem 110:513-523, 2010), which in turn leads to different ECD fragmentation behavior and mechanisms. Our results are in good agreement with previously published ab initio calculations on Se-Se compounds by other groups.
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Affiliation(s)
- Huilin Li
- Department of Chemistry, University of Warwick, Coventry, UK
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Gámez JA, Yáñez M. Electron Attachment to Diselenides Revisited: Se–Se Bond Cleavage Is Neither Adiabatic nor the Most Favorable Process. J Chem Theory Comput 2011; 7:1726-35. [DOI: 10.1021/ct2002286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- José A. Gámez
- Departamento de Química, Módulo 13, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049-Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049-Madrid, Spain
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6
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Gámez JA, Yáñez M. Is Se–Se bond cleavage the most favourable process in electron attachment to diselenides? The importance of asymmetry. Chem Commun (Camb) 2011; 47:3939-41. [DOI: 10.1039/c0cc04675b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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7
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Gámez JA, Yáñez M. Asymmetry and Electronegativity in the Electron Capture Activation of the Se−Se Bond: σ*(Se−Se) vs σ*(Se−X). J Chem Theory Comput 2010; 6:3102-12. [DOI: 10.1021/ct100336q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José A. Gámez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
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8
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Song MX, Zhao ZX, Bai FQ, Liu YJ, Zhang HX, Sun CC. CASSCF/CASPT2 Calculation of the Low-Lying Electronic States of the CH3Se Neutral Radical and Its Cation. J Phys Chem A 2010; 114:7173-8. [DOI: 10.1021/jp102321c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ming-Xing Song
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Zeng-Xia Zhao
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Fu-Quan Bai
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Yue-Jie Liu
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Hong-Xing Zhang
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Chia-chung Sun
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People's Republic of China
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10
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Meija J. Mathematical tools in analytical mass spectrometry. Anal Bioanal Chem 2006; 385:486-99. [PMID: 16514517 DOI: 10.1007/s00216-006-0298-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 12/14/2005] [Accepted: 01/05/2006] [Indexed: 10/25/2022]
Abstract
Over the last few decades, mass spectrometry has become a powerful tool for exploring various aspects of molecular processes occurring in biological systems. Such exploration is leading to a greater understanding of various complex life processes; unraveling these processes poses the greatest challenge to contemporary bioscience. With due respect to sample preparation, data analysis is rapidly becoming a major obstacle to the conversion of experimental knowledge into valid conclusions. It is interesting to note that many problems related to mass spectrometry can be solved using techniques from computer science, graph theory and discrete mathematics. The aim of this manuscript is to recollect several essays that demonstrate the power and the need to apply such skills to mass spectrometry data interpretation. Special attention is paid to situations where traditional chemical analysis reaches its limits but mathematical reasoning can still allow us to reach valid conclusions.
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Affiliation(s)
- Juris Meija
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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Sun Q, Li Z, Zeng X, Wang W, Sun Z, Ge M, Wang D, Mok DKW, Chau FT. First experimental observation of the CH3Se radical. Chemphyschem 2005; 6:2032-5. [PMID: 16178040 DOI: 10.1002/cphc.200500150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Qiao Sun
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China
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Meija J, Centineo G, Ignacio Garcia Alonso J, Sanz-Medel A, Caruso JA. Interpretation of butyltin mass spectra using isotope pattern reconstruction for the accurate measurement of isotope ratios from molecular clusters. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:807-14. [PMID: 15948232 DOI: 10.1002/jms.855] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The fragmentation patterns of butyltin compounds (mono-, di-, and tributyltin) in an electron impact ion source were studied using an isotope pattern reconstruction algorithm with emphasis on isotope ratio measurements from molecular clusters. For this purpose, standards of natural tin isotope abundance and a (119)Sn-enriched mixture of the three compounds were both ethylated and propylated using sodium tetraalkylborates. The corresponding mass spectra of the various tetraalkyltin compounds prepared were obtained by GC/MS after their extraction with hexane. The results showed that pure interference-free molecular clusters were obtained only for certain R(3)Sn(+) ions where no isobaric overlap with R(2)SnH(+) ions occurred (e.g. BuEt(2)Sn(+) overlaps with Bu(2)SnH(+)). These ions are ideal candidates for accurate Sn isotope ratio measurements, while isotope pattern perturbing interferences are observed for other molecular fragments down to Sn(.)(+). Isotope pattern reconstruction algorithm thus can be used as an analytical tool to ensure the absence of molecular interferences--a requirement for accurate isotope ratio measurements from molecular clusters. The relevance of these studies for the determination of butyltin compounds in environmental samples by isotope dilution GC/MS is also discussed.
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Affiliation(s)
- Juris Meija
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
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