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Combinatorial Approaches for Mass Spectra Recalibration
2008
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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Algorithms for recalibrating mass spectra have to be robust with respect to wrongly assigned peaks, as well as efficient due to the amount of mass spectrometry data. ...
The recalibration of mass spectra leads us to the problem of finding an optimal matching between mass spectra under measurement errors. ...
ACKNOWLEDGMENTS The authors wish to thank Tobias Marschall and Marcel Martin for implementing the algorithms and running the experiments. ...
doi:10.1109/tcbb.2007.1077
pmid:18245878
fatcat:mctehu4igrakhlbaca3oiazy3a
Spectral Dictionaries
2008
Molecular & Cellular Proteomics
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Database search tools identify peptides by matching tandem mass spectra against a protein database. ...
We present a new MS-Dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that MS-Dictionary can identify spectra that are missed in the database search. ...
Acknowledgments-We thank Vineet Bafna, Ari Frank, Sam Payne, and Stephen Tanner for useful discussions. We thank Steve Briggs and Dick Smith for sharing MS/MS data generated in their laboratories. ...
doi:10.1074/mcp.m800103-mcp200
pmid:18703573
pmcid:PMC2621003
fatcat:rrjgewpa4jhaxm5mjprdqlpmhu
Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins
2010
Molecular & Cellular Proteomics
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This raises both pattern recognition and combinatorial challenges for spectral deconvolution. We present MS-Deconv, a combinatorial algorithm for spectral deconvolution. ...
Because tandem mass spectra of intact proteins are very complex, spectral deconvolution (grouping peaks into isotopomer envelopes) is a key initial stage for their interpretation. ...
Although this approach often generates reasonable sets of envelopes for simple spectra, its performance deteriorates in cases of complex spectra. ...
doi:10.1074/mcp.m110.002766
pmid:20855543
pmcid:PMC3101958
fatcat:z2sdufmzona2pnjgkfrpc7nc7u
Preview: A Program for Surveying Shotgun Proteomics Tandem Mass Spectrometry Data
2011
Analytical Chemistry
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Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. ...
Moreover, Preview optionally recalibrates mass-over-charge measurements, leading to further improvement in identification results. ...
and then corrects for the number of false hits estimated by the target/decoy approach. ...
doi:10.1021/ac200609a
pmid:21619057
pmcid:PMC3134881
fatcat:dbml66vh4ze2pcpb64lrnhmmrm
Fragmentation trees reloaded
[article]
2015
arXiv
pre-print
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Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. ...
We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a maximum a posteriori estimator. ...
(Santa Clara, USA) for providing uncorrected peak lists of their spectral library. ...
arXiv:1412.1929v3
fatcat:so33wxlacbh5dnxamegppk6xom
Fragmentation trees reloaded
2016
Journal of Cheminformatics
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Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. ...
Results: We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. ...
We also thank Emma Schymanski and Michael Stravs for providing their data. ...
doi:10.1186/s13321-016-0116-8
pmid:26839597
pmcid:PMC4736045
fatcat:i7h27ibosvgubcn3yy75qgkqhq
Fragmentation Trees Reloaded
[chapter]
2015
Lecture Notes in Computer Science
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Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. ...
Results: We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. ...
We also thank Emma Schymanski and Michael Stravs for providing their data. ...
doi:10.1007/978-3-319-16706-0_10
fatcat:p2g43bl6jbcwbcpwcnxld2fur4
CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction
2018
Journal of Proteome Research
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Coeluting peptides are still a major challenge for the identification and validation of MS/MS spectra, but carry great potential. ...
For highresolution data sets this workflow identifies 38−64% chimeric spectra, which results in up to 63% more unique peptides compared to a conventional single search strategy. ...
Recalibration can be done for measured deviations of m/z values, Δ ( ) m z , as well as for relative mass deviations, Δm ppm . ...
doi:10.1021/acs.jproteome.7b00836
pmid:29863353
pmcid:PMC6079931
fatcat:ojslet4j2rehpadinv5rdob2pi
Low mass di-electrons from Cu+Cu Collisions
2011
Zenodo
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By studying the Cu+Cu mass spectra and yields as a function of pair pT and collision centrality we obtain further understanding of its behavior. ...
Finally, the mass and p T region for the combinatorial normalization is adjusted. ...
Figure 4.8 show the generated combinatorial backgrounds for the dielectron mass spectra using fifty groups divided according to ten centrality and five z-vertex classifications. ...
doi:10.5281/zenodo.4404683
fatcat:7qaza64kczczparndnxrtrfrfq
High-Throughput Small Molecule Identification Using MALDI-TOF and a Nanolayered Substrate
2011
Analytical Chemistry
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An internal recalibration algorithm also significantly improved mass accuracy to as low as 45 ppm. ...
Our study lays the foundation for improved encoderless combinatorial chemistry. ...
Moffitt for editing, and Linda Keys and Eugenia Trabucchi for administrative assistance. ...
doi:10.1021/ac2006735
pmid:21651231
pmcid:PMC3128203
fatcat:q2d5gorhx5cizao6x4evmlf5fu
Critical Assessment of Small Molecule Identification 2016: automated methods
2017
Journal of Cheminformatics
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The machine learning and chemistry-based approaches are shown to perform in complementary ways. ...
The achieved high rates of correct candidates in the Top 1 and Top 10, despite large candidate numbers, open up great possibilities for high-throughput annotation of untargeted analysis for "known unknowns ...
We thank the reviewers for their comments and suggestions. ...
doi:10.1186/s13321-017-0207-1
pmid:29086042
pmcid:PMC5368104
fatcat:uuvqxmusujhijjpmanptzbkj3i
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
2019
Nature Methods
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We report SIRIUS 4 (https://bio.informatik.uni-jena.de/sirius/), which provides a fast computational approach for molecular structure identification. ...
Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging. ...
SIRIUS 4: Turning tandem mass spectra into metabolite structure information ...
doi:10.1038/s41592-019-0344-8
pmid:30886413
fatcat:qtx2fo5cobcgponth6pqhzqzbe
Analysis of functional groups in atmospheric aerosols by infrared spectroscopy: systematic intercomparison of calibration methods for US measurement network samples
2019
Atmospheric Measurement Techniques
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</strong> Peak fitting (PF) and partial least squares (PLS) regression have been independently developed for estimation of functional groups (FGs) from Fourier transform infrared (FTIR) spectra of ambient ...
In evaluating state-of-the-art methods for FG abundance by FTIR, we suggest directions for future research.</p> ...
We also thank Christophe Delval for assistance in identification of the Christiansen peak species. Review statement. This paper was edited by Charles Brock and reviewed by two anonymous referees. ...
doi:10.5194/amt-12-2287-2019
fatcat:cnyus2ml4ndatbwmsfbgqoosuu
Generation of a Collision Cross Section Library for Multi-Dimensional Plant Metabolomics Using UHPLC-Trapped Ion Mobility-MS/MS
2019
Metabolites
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Here, we report a combinatorial solution to aid in both grand challenges using UHPLC-trapped ion mobility spectrometry coupled to tandem mass spectrometry (UHPLC-TIMS-TOF-MS). ...
of the UHPLC-TIMS-TOF-MS/MS in metabolomics was then demonstrated using extracts from the model legume Medicago truncatula and metabolites were confidently identified based on retention time, accurate mass ...
, Niels Goedecke, Niko Kessler for technical support; Vladimir Ondruska for repairs; and all of Bruker for assistance in instrument upkeep maintenance and speedy responses. ...
doi:10.3390/metabo10010013
pmid:31878231
pmcid:PMC7023306
fatcat:mhvjxglnu5gbbmydrvciggepvm
Reduction of measurement noise in a continuous glucose monitor by coating the sensor with a zwitterionic polymer
2018
Nature Biomedical Engineering
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Here, we show that coating the sensor with a zwitterionic polymer, found via a combinatorial-chemistry approach, significantly reduces signal noise and improves CGM performance. ...
We evaluated the polymer-coated sensors in mice as well as in healthy and diabetic non-human primates, and show that the sensors accurately record glucose levels without the need for recalibration. ...
High resolution mass spectral (HRMS) data were obtained on 7 Tesk Bruker Fourier-Transform Ion Cyclotron Resonance Mass Spectrometer. ...
doi:10.1038/s41551-018-0273-3
pmid:30931173
pmcid:PMC6436621
fatcat:mpz2hcmmeba5holozhw54zns44
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