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Combinatorial Approaches for Mass Spectra Recalibration

S. Bocker, V. Makinen
2008 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

Sangtae Kim, Nitin Gupta, Nuno Bandeira, Pavel A. Pevzner
2008 Molecular & Cellular Proteomics  
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

Xiaowen Liu, Yuval Inbar, Pieter C. Dorrestein, Colin Wynne, Nathan Edwards, Puneet Souda, Julian P. Whitelegge, Vineet Bafna, Pavel A. Pevzner
2010 Molecular & Cellular Proteomics  
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

Yong J. Kil, Christopher Becker, Wendy Sandoval, David Goldberg, Marshall Bern
2011 Analytical Chemistry  
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]

Kai Dührkop, Sebastian Böcker
2015 arXiv   pre-print
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

Sebastian Böcker, Kai Dührkop
2016 Journal of Cheminformatics  
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]

Kai Dührkop, Sebastian Böcker
2015 Lecture Notes in Computer Science  
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

Viktoria Dorfer, Sergey Maltsev, Stephan Winkler, Karl Mechtler
2018 Journal of Proteome Research  
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

Sarah C. Campbell
2011 Zenodo  
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

Jeong Heon Lee, Hak Soo Choi, Khaled A. Nasr, Miyoung Ha, Yangsun Kim, John V. Frangioni
2011 Analytical Chemistry  
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

Emma L. Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker, Juho Rousu, Huibin Shen (+5 others)
2017 Journal of Cheminformatics  
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

Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V. Melnik, Marvin Meusel, Pieter C. Dorrestein, Juho Rousu, Sebastian Böcker
2019 Nature Methods  
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

Matteo Reggente, Ann M. Dillner, Satoshi Takahama
2019 Atmospheric Measurement Techniques  
</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

Mark Schroeder, Sven W. Meyer, Heino M. Heyman, Aiko Barsch, Lloyd W. Sumner
2019 Metabolites  
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

Xi Xie, Joshua C. Doloff, Volkan Yesilyurt, Atieh Sadraei, James J. McGarrigle, Mustafa Omami, Omid Veiseh, Shady Farah, Douglas Isa, Sofia Ghani, Ira Joshi, Arturo Vegas (+11 others)
2018 Nature Biomedical Engineering  
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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