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HIGH-ACCURACY PEAK PICKING OF PROTEOMICS DATA USING WAVELET TECHNIQUES

EVA LANGE, CLEMENS GRÖPL, KNUT REINERT, OLIVER KOHLBACHER, ANDREAS HILDEBRANDT
2005 Biocomputing 2006  
A new peak picking algorithm for the analysis of mass spectrometric (MS) data is presented.  ...  SNAP, Apex) our algorithm is able to separate overlapping peaks of multiply charged peptides in ESI-MS data of low resolution.  ...  Johan Gobom, Max-Planck-Institute for Molecular Genetics, Berlin for providing data set B, and Michael Kerber who was involved in the implementation of an early version of the algorithm.  ... 
doi:10.1142/9789812701626_0023 fatcat:ewrutcsp65fjjl3da6atexiwzq

MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

Viktoria Dorfer, Peter Pichler, Thomas Stranzl, Johannes Stadlmann, Thomas Taus, Stephan Winkler, Karl Mechtler
2014 Journal of Proteome Research  
for high mass accuracy.  ...  The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification  ...  We here describe MS Amanda, a novel database search engine, specially developed for high-resolution tandem mass spectrometry data, taking advantage of high mass accuracy and considering fragment ion intensities  ... 
doi:10.1021/pr500202e pmid:24909410 pmcid:PMC4119474 fatcat:56bkhmbjnzeb3gsftdkvhwo7gm

Modeling Mass Spectrometry-Based Protein Analysis [chapter]

Jan Eriksson, David Fenyö
2010 Msphere  
The success of mass spectrometry based proteomics depends on efficient methods for data analysis. These methods require a detailed understanding of the information value of the data.  ...  Here, we describe how the information value can be elucidated by performing simulations using synthetic data.  ...  Acknowledgments This work was supported by funding provided by the National Institutes of Health Grants CA126485, DE018385, NS050276, RR00862 and RR022220, the Carl Trygger foundation, and the Swedish  ... 
doi:10.1007/978-1-60761-977-2_8 pmid:21082431 pmcid:PMC3757507 fatcat:vhgt36toazgnrmc4twdnjqpguq

SparseCodePicking: feature extraction in mass spectrometry using sparse coding algorithms [article]

Theodore Alexandrov, Klaus Steinhorst, Oliver Keszoecze, Stefan Schiffler
2009 arXiv   pre-print
A crucial step of MS data processing is the peak picking which selects peaks containing information about molecules with high concentrations which are of interest in an MS investigation.  ...  We present a new procedure of the peak picking based on a sparse coding algorithm.  ...  Therefore, peak picking is usually a starting and a crucial step of MS data analysis. There exist various methods of peak picking but they are still far from perfect [6] .  ... 
arXiv:0907.3426v2 fatcat:zyup37zqnfajvdarjsctqdc5li

On the Proper Use of Mass Accuracy in Proteomics: Fig. 1

Roman Zubarev, Matthias Mann
2006 Molecular & Cellular Proteomics  
Proper use of high mass accuracy data can make MS-based proteomics one of the most "digital" and accurate post-genomics disciplines.  ...  More advanced uses of high mass accuracy include an MMD that depends on the signal abundance of each peptide. Adapting search engines to high mass accuracy in the MS/MS data is also a high priority.  ...  spectrum in which the peak was "picked" for sequencing and where it is often very weak.  ... 
doi:10.1074/mcp.m600380-mcp200 pmid:17164402 fatcat:go54uelh2fg43a45gbughs4m3m

EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data

Chalini D. Wijetunge, Isaam Saeed, Berin A. Boughton, Jeffrey M. Spraggins, Richard M. Caprioli, Antony Bacic, Ute Roessner, Saman K. Halgamuge
2015 Bioinformatics  
We further demonstrate the performance of our peak picking method over other traditional approaches by using a publicly available MALDI-IMS proteomics dataset of a rat brain.  ...  Various data processing methods have been developed for exploring the resultant high volume data.  ...  Acknowledgements The authors thank the University of Melbourne-Vanderbilt University Partnership Grant Scheme and also the School of Botany node of Metabolomics Australia (MA) at The University of Melbourne  ... 
doi:10.1093/bioinformatics/btv356 pmid:26063840 fatcat:75lyjpho65godhmuf7kfznp7ri

Tools for Label-free Peptide Quantification

Sven Nahnsen, Chris Bielow, Knut Reinert, Oliver Kohlbacher
2012 Molecular & Cellular Proteomics  
The increasing scale and complexity of quantitative proteomics studies complicate subsequent analysis of the acquired data.  ...  We review the state of the art with respect to computational tools for label-free quantification in untargeted proteomics.  ...  The advent of high-resolution mass spectrometers has made the signal processing and peak picking tasks simpler than they were on low-resolution instruments.  ... 
doi:10.1074/mcp.r112.025163 pmid:23250051 pmcid:PMC3591650 fatcat:7otlf6bpnrginfkaihiprxsljq

IDPQuantify: Combining Precursor Intensity with Spectral Counts for Protein and Peptide Quantification

Yao-Yi Chen, Matthew C. Chambers, Ming Li, Amy-Joan L. Ham, Jeffrey L. Turner, Bing Zhang, David L. Tabb
2013 Journal of Proteome Research  
The software is able to associate peptides with peaks that are otherwise left unidentified to increase the efficiency of protein quantification, especially for low-abundance proteins.  ...  We have applied IDPQuantify to three comparative proteomic datasets featuring gold standard protein differences spiked in complicated backgrounds.  ...  Best peaks for peptides were picked at peak width tolerance of 3 standard deviations between peak time and peak retention time, with average peak picking at an FDR of 5%.  ... 
doi:10.1021/pr400438q pmid:23879310 pmcid:PMC3804902 fatcat:ex7zguvuifgzxb5ugnyxw4o6zm

Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard's msConvert

William R. French, Lisa J. Zimmerman, Birgit Schilling, Bradford W. Gibson, Christine A. Miller, R. Reid Townsend, Stacy D. Sherrod, Cody R. Goodwin, John A. McLean, David L. Tabb
2014 Journal of Proteome Research  
We report the implementation of high-quality signal processing algorithms into ProteoWizard, an efficient, open-source software package designed for analyzing proteomics tandem mass spectrometry data.  ...  The mass accuracy of matched precursor ions also compared favorably with vendor and commercial tools.  ...  for sharing the Waters yeast data, Roy Martin for providing the K562 cell lysate data from the Waters Synapt G2-S, John Cottrell for assisting us with evaluation licenses of Mascot Distiller, and John  ... 
doi:10.1021/pr500886y pmid:25411686 pmcid:PMC4324452 fatcat:l3keu7uklnfwdgxjh5ynw3fehi

Automated Protein Turnover Calculations from 15N Partial Metabolic Labeling LC/MS Shotgun Proteomics Data

David Lyon, Maria Angeles Castillejo, Christiana Staudinger, Wolfram Weckwerth, Stefanie Wienkoop, Volker Egelhofer, Lennart Martens
2014 PLoS ONE  
Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples.  ...  Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies.  ...  -All subsequent peaks are picked analogously (since the mass accuracy decreases with decreasing intensity, this value can also be adjusted separately by the user dependent on the given data).  ... 
doi:10.1371/journal.pone.0094692 pmid:24736476 pmcid:PMC3988089 fatcat:h7qwynge45hebbacijtzbuold4

Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

Jürgen Cox, Matthias Mann
2009 Journal of the American Society for Mass Spectrometry  
Precision proteomics requires high-resolution and high mass accuracy peptide measurements.  ...  The deviation of mass values determined from charge pairs is used to convert mass precision to mass accuracy for subsequent database search.  ...  Acknowledgments The authors thank all the other members of the Proteomics and Signal Transduction group for help with the development of Appendix A Supplementary Material Supplementary material associated  ... 
doi:10.1016/j.jasms.2009.05.007 pmid:19553133 fatcat:t7rnm247ejbdlelddayllcmvva

Accurate Identification of Deamidated Peptides in Global Proteomics Using a Quadrupole Orbitrap Mass Spectrometer

Angelito I. Nepomuceno, Radiance J. Gibson, Shan M. Randall, David C. Muddiman
2013 Journal of Proteome Research  
For proper assignment, it is inherently important to use a mass spectrometer with high mass measurement accuracy and high resolving power.  ...  Mass spectral analysis of deamidated peptides is complicated and often misassigned due to overlapping (13)C peak of the amidated form with the deamidated monoisotopic peak; these two peaks are only separated  ...  Nagendran Muthusamy from NCSU College of Veterinary Medicine for providing the mouse tissue samples.  ... 
doi:10.1021/pr400848n pmid:24289162 pmcid:PMC3976439 fatcat:6dysuwvhrjahrgzruyhjsavjbm

A New Algorithm Using Cross-Assignment for Label-Free Quantitation with LC−LTQ-FT MS

Victor P. Andreev, Lingyun Li, Lei Cao, Ye Gu, Tomas Rejtar, Shiaw-Lin Wu, Barry L. Karger
2007 Journal of Proteome Research  
Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory.  ...  Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQFT MS mass spectrometer (or other high resolution mass spectrometers, such as a Q-TOF MS).  ...  The authors thank one of the reviewers for suggesting the format of Fig. 2 . This is contribution number 900 from the Barnett Institute.  ... 
doi:10.1021/pr0606880 pmid:17441747 pmcid:PMC2563808 fatcat:afmpdajiozgrbfoi72ievydswi

Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

Jesper V. Olsen, Lyris M. F. de Godoy, Guoqing Li, Boris Macek, Peter Mortensen, Reinhold Pesch, Alexander Makarov, Oliver Lange, Stevan Horning, Matthias Mann
2005 Molecular & Cellular Proteomics  
High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification.  ...  For tandem mass spectra we demonstrate similarly high mass accuracy and discuss its impact on database searching.  ...  Acknowledgments-We thank colleagues in the Department for Proteomics and Cell Signaling as well as at the Beijing Genome Institute for fruitful discussions.  ... 
doi:10.1074/mcp.t500030-mcp200 pmid:16249172 fatcat:cpnxjvhtbjct3gjuw2fzvevrm4

High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe [article]

Vadim Demichev, Fengchao Yu, Guo Ci Teo, Lukasz Szyrwiel, George Rosenberger, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S. Lilley, Michael Muelleder, Alexey I. Nesvizhskii, Markus Ralser
2021 bioRxiv   pre-print
The dia-PASEF technology exploits ion mobility separation for high-sensitivity analysis of complex proteomes.  ...  Hence, the combination of FragPipe and DIA-NN provides a simple-to-use software platform for dia-PASEF data analysis, yielding significant gains in high-sensitivity proteomics.  ...  Acknowledgements We thank Sven Brehmer and Nagarjuna Nagaraj (Bruker) for helpful discussions and their advice on the analysis of dia-PASEF data.  ... 
doi:10.1101/2021.03.08.434385 fatcat:frbx6yifczcwlmkkuw34ty2zza
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