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Article ; Online: Correction: Cumulant mapping as the basis of multi-dimensional spectrometry.

Frasinski, Leszek J

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 47, Page(s) 32726

Abstract: Correction for 'Cumulant mapping as the basis of multi-dimensional spectrometry' by Leszek J. Frasinski, ...

Abstract	Correction for 'Cumulant mapping as the basis of multi-dimensional spectrometry' by Leszek J. Frasinski,
Language	English
Publishing date	2023-12-06
Publishing country	England
Document type	Published Erratum
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp90213g
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cumulant mapping as the basis of multi-dimensional spectrometry.

Frasinski, Leszek J

Physical chemistry chemical physics : PCCP

2022 Volume 24, Issue 35, Page(s) 20776–20787

Abstract: Cumulant mapping employs a statistical reconstruction of the whole by sampling its parts. The theory developed in this work formalises and ... ...

Abstract	Cumulant mapping employs a statistical reconstruction of the whole by sampling its parts. The theory developed in this work formalises and extends
MeSH term(s)	Models, Theoretical ; Spectrometry, Fluorescence/methods
Language	English
Publishing date	2022-09-14
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d2cp02365b
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Article ; Online: Identification of Cofragmented Combinatorial Peptide Isomers by Two-Dimensional Partial Covariance Mass Spectrometry.

Driver, Taran / Pipkorn, Rüdiger / Averbukh, Vitali / Frasinski, Leszek J / Marangos, Jon P / Edelson-Averbukh, Marina

Journal of the American Society for Mass Spectrometry

2023 Volume 34, Issue 7, Page(s) 1230–1234

Abstract: Combinatorial post-translational modifications (PTMs), such as those forming the so-called "histone code", have been linked to cell differentiation, embryonic development, cellular reprogramming, aging, cancers, neurodegenerative disorders, ...

Abstract	Combinatorial post-translational modifications (PTMs), such as those forming the so-called "histone code", have been linked to cell differentiation, embryonic development, cellular reprogramming, aging, cancers, neurodegenerative disorders,
MeSH term(s)	Humans ; Peptides/chemistry ; Mass Spectrometry/methods ; Histones/chemistry ; Histone Code ; Protein Processing, Post-Translational
Chemical Substances	Peptides ; Histones
Language	English
Publishing date	2023-05-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.3c00111
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Article: Two-Dimensional Partial Covariance Mass Spectrometry for the Top–Down Analysis of Intact Proteins

Driver, Taran / Averbukh, Vitali / Frasiński, Leszek J. / Marangos, Jon P. / Edelson-Averbukh, Marina

Analytical chemistry. 2021 July 26, v. 93, no. 31

2021

Abstract: Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation ... ...

Abstract	Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment–fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment–fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the in silico deconvolution of the overlapping fragment ion signals from two co-isolated and co-fragmented intact proteins, demonstrating a viable new method for the concurrent mass spectrometric identification of a mixture of intact protein ions from the same fragment ion spectrum.
Keywords	analytical chemistry ; computer simulation ; covariance ; peptides ; tandem mass spectrometry
Language	English
Dates of publication	2021-0726
Size	p. 10779-10788.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00332
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Article ; Online: Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry.

Driver, Taran / Bachhawat, Nikhil / Frasinski, Leszek J / Marangos, Jonathan P / Averbukh, Vitali / Edelson-Averbukh, Marina

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 12

Abstract: The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called ` ...

Abstract	The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra', which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce '3-57 chimera tag' technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.
MeSH term(s)	Databases, Protein ; Ions/metabolism ; Peptides/metabolism ; Proteomics/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Ions ; Peptides
Language	English
Publishing date	2021-06-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26123728
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Article ; Online: Two-Dimensional Partial Covariance Mass Spectrometry for the Top-Down Analysis of Intact Proteins.

Driver, Taran / Averbukh, Vitali / Frasiński, Leszek J / Marangos, Jon P / Edelson-Averbukh, Marina

Analytical chemistry

2021 Volume 93, Issue 31, Page(s) 10779–10788

Abstract	Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment-fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment-fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the
MeSH term(s)	Ions ; Peptides ; Proteins ; Proteomics ; Tandem Mass Spectrometry
Chemical Substances	Ions ; Peptides ; Proteins
Language	English
Publishing date	2021-07-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00332
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Article: Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry

Driver, Taran / Bachhawat, Nikhil / Pipkorn, Rüdiger / Frasiński, Leszek J. / Marangos, Jon P. / Edelson-Averbukh, Marina / Averbukh, Vitali

Analytical chemistry. 2021 Nov. 01, v. 93, no. 45

2021

Abstract: We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement ... ...

Abstract	We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural specificity afforded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides, the 2D-PC-MS correlation-matching procedure is based on complementary and internal ion correlations, the identification of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.
Keywords	amino acid sequences ; analytical chemistry ; covariance ; databases ; mass spectrometry ; peptides ; proteomics
Language	English
Dates of publication	2021-1101
Size	p. 14946-14954.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00895
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Article ; Online: Efficient prediction of attosecond two-colour pulses from an X-ray free-electron laser with machine learning.

Alaa El-Din, Karim K / Alexander, Oliver G / Frasinski, Leszek J / Mintert, Florian / Guo, Zhaoheng / Duris, Joseph / Zhang, Zhen / Cesar, David B / Franz, Paris / Driver, Taran / Walter, Peter / Cryan, James P / Marinelli, Agostino / Marangos, Jon P / Mukherjee, Rick

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7267

Abstract: X-ray free-electron lasers are sources of coherent, high-intensity X-rays with numerous applications in ultra-fast measurements and dynamic structural imaging. Due to the stochastic nature of the self-amplified spontaneous emission process and the ... ...

Abstract	X-ray free-electron lasers are sources of coherent, high-intensity X-rays with numerous applications in ultra-fast measurements and dynamic structural imaging. Due to the stochastic nature of the self-amplified spontaneous emission process and the difficulty in controlling injection of electrons, output pulses exhibit significant noise and limited temporal coherence. Standard measurement techniques used for characterizing two-coloured X-ray pulses are challenging, as they are either invasive or diagnostically expensive. In this work, we employ machine learning methods such as neural networks and decision trees to predict the central photon energies of pairs of attosecond fundamental and second harmonic pulses using parameters that are easily recorded at the high-repetition rate of a single shot. Using real experimental data, we apply a detailed feature analysis on the input parameters while optimizing the training time of the machine learning methods. Our predictive models are able to make predictions of central photon energy for one of the pulses without measuring the other pulse, thereby leveraging the use of the spectrometer without having to extend its detection window. We anticipate applications in X-ray spectroscopy using XFELs, such as in time-resolved X-ray absorption and photoemission spectroscopy, where improved measurement of input spectra will lead to better experimental outcomes.
Language	English
Publishing date	2024-03-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-56782-z
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Article ; Online: Multiparticle Cumulant Mapping for Coulomb Explosion Imaging.

Cheng, Chuan / Frasinski, Leszek J / Moğol, Gönenç / Allum, Felix / Howard, Andrew J / Rolles, Daniel / Bucksbaum, Philip H / Brouard, Mark / Forbes, Ruaridh / Weinacht, Thomas

Physical review letters

2023 Volume 130, Issue 9, Page(s) 93001

Abstract: We extend covariance velocity map ion imaging to four particles, establishing cumulant mapping and allowing for measurements that provide insights usually associated with coincidence detection, but at much higher count rates. Without correction, a ... ...

Abstract	We extend covariance velocity map ion imaging to four particles, establishing cumulant mapping and allowing for measurements that provide insights usually associated with coincidence detection, but at much higher count rates. Without correction, a fourfold covariance analysis is contaminated by the pairwise correlations of uncorrelated events, but we have addressed this with the calculation of a full cumulant, which subtracts pairwise correlations. We demonstrate the approach on the four-body breakup of formaldehyde following strong field multiple ionization in few-cycle laser pulses. We compare Coulomb explosion imaging for two different pulse durations (30 and 6 fs), highlighting the dynamics that can take place on ultrafast timescales. These results have important implications for Coulomb explosion imaging as a tool for studying ultrafast structural changes in molecules, a capability that is especially desirable for high-count-rate x-ray free-electron laser experiments.
Language	English
Publishing date	2023-02-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.130.093001
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Article ; Online: Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry.

Driver, Taran / Bachhawat, Nikhil / Pipkorn, Rüdiger / Frasiński, Leszek J / Marangos, Jon P / Edelson-Averbukh, Marina / Averbukh, Vitali

Analytical chemistry

2021 Volume 93, Issue 45, Page(s) 14946–14954

Abstract	We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural specificity afforded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides, the 2D-PC-MS correlation-matching procedure is based on complementary and internal ion correlations, the identification of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.
MeSH term(s)	Databases, Protein ; Mass Spectrometry ; Peptides ; Proteomics ; Search Engine
Chemical Substances	Peptides
Language	English
Publishing date	2021-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00895
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