Publications by authors named "David L Tabb"

100Publications

Dysregulated healing responses in diabetic wounds occur in the early stages post injury.

J Mol Endocrinol 2020 Dec 1. Epub 2020 Dec 1.

M van de Vyver, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa.

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December 2020

Interrogating Fractionation and Other Sources of Variability in Shotgun Proteomes Using Quality Metrics.

Proteomics 2020 11 23;20(21-22):e1900382. Epub 2020 Aug 23.

SATBBI (South African Tuberculosis Bioinformatics Initiative), Centre for Bioinformatics and Computational Biology, Stellenbosch University, Cape Town, 7505, South Africa.

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November 2020

Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment.

Methods Mol Biol 2018 ;1789:205-220

Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.

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February 2019

A Serum Circulating miRNA Signature for Short-Term Risk of Progression to Active Tuberculosis Among Household Contacts.

Front Immunol 2018 13;9:661. Epub 2018 Apr 13.

DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.

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June 2019

Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World.

J Biomol Tech 2018 04 23;29(1):4-15. Epub 2018 Mar 23.

Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.

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April 2018

Sipros Ensemble improves database searching and filtering for complex metaproteomics.

Bioinformatics 2018 03;34(5):795-802

Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.

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March 2018

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.

J Proteome Res 2017 10 11;16(10):3841-3851. Epub 2017 Sep 11.

DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa.

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October 2017

Quality control in mass spectrometry-based proteomics.

Mass Spectrom Rev 2018 09 7;37(5):697-711. Epub 2017 Sep 7.

Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.

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September 2018

The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.

Anal Chem 2017 04 30;89(8):4474-4479. Epub 2017 Mar 30.

Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences , Tygerberg Hospital, Francie Van Zijl Drive, Cape Town 7505, South Africa.

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April 2017

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

J Proteomics 2017 01 4;150:170-182. Epub 2016 Aug 4.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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January 2017

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Nat Methods 2016 Aug 27;13(8):651-656. Epub 2016 Jun 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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August 2016

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Anal Chem 2016 06 24;88(11):5733-41. Epub 2016 May 24.

Department of Biomedical Informatics, Vanderbilt University , Nashville, Tennessee 37203, United States.

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June 2016

Site-Specific N-Glycosylation Characterization of Windmill Palm Tree Peroxidase Using Novel Tools for Analysis of Plant Glycopeptide Mass Spectrometry Data.

J Proteome Res 2016 06 19;15(6):2026-38. Epub 2016 May 19.

Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States.

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June 2016

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.

Mol Cell Proteomics 2016 Mar 11;15(3):1164-75. Epub 2015 Dec 11.

From the ‡Department of Biomedical Informatics, ‖Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232;

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March 2016

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry.

J Proteome Res 2016 Jan 9;15(1):245-58. Epub 2015 Dec 9.

Department of Medicine, Division of Nephrology and Hypertension, ‡Center for Matrix Biology, §Department of Biochemistry, and ⊥Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee 37232, United States.

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January 2016

Correcting systematic bias and instrument measurement drift with mzRefinery.

Bioinformatics 2015 Dec 4;31(23):3838-40. Epub 2015 Aug 4.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and.

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December 2015

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

J Proteome Res 2015 Sep 21;14(9):3555-67. Epub 2015 Jul 21.

Department of Biomedical Informatics, Vanderbilt University , Nashville, Tennessee 37203, United States.

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September 2015

The SEQUEST family tree.

Authors:
David L Tabb

J Am Soc Mass Spectrom 2015 Nov 30;26(11):1814-9. Epub 2015 Jun 30.

School of Medicine, Vanderbilt University, Nashville, TN, 37232-8575, USA.

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November 2015

Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Sci Data 2015 23;2:150022. Epub 2015 Jun 23.

Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, TN 37232, USA ; Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center , Nashville, TN 37232, USA.

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December 2015

Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.

J Proteome Res 2015 Feb 2;14(2):1299-307. Epub 2014 Dec 2.

Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee 37232-8340, United States.

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February 2015

Proteogenomic characterization of human colon and rectal cancer.

Nature 2014 Sep 20;513(7518):382-7. Epub 2014 Jul 20.

1] Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232, USA.

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September 2014

Employing ProteoWizard to Convert Raw Mass Spectrometry Data.

Curr Protoc Bioinformatics 2014 Jun 17;46:13.24.1-9. Epub 2014 Jun 17.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.

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June 2014

QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics.

Anal Chem 2014 Mar 17;86(5):2497-509. Epub 2014 Feb 17.

Department of Mathematical Sciences, University of Cincinnati , Cincinnati, Ohio 45221, United States.

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March 2014

IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification.

J Proteome Res 2013 Sep 12;12(9):4111-21. Epub 2013 Aug 12.

Department of Biomedical Informatics, Vanderbilt University Medical School, Nashville, Tennessee 37232-8575, United States.

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September 2013

Informatics of protein and posttranslational modification detection via shotgun proteomics.

Methods Mol Biol 2013 ;1002:167-79

Vanderbilt University Medical Center, Nashville, TN, USA.

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February 2014

Basophile: accurate fragment charge state prediction improves peptide identification rates.

Genomics Proteomics Bioinformatics 2013 Apr 8;11(2):86-95. Epub 2013 Mar 8.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

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April 2013

Quality assessment for clinical proteomics.

Authors:
David L Tabb

Clin Biochem 2013 Apr 12;46(6):411-20. Epub 2012 Dec 12.

Department of Biomedical Informatics, Vanderbilt University, USA.

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April 2013

Mapping serum albumin adducts of the food-borne carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine by data-dependent tandem mass spectrometry.

Chem Res Toxicol 2012 Oct 14;25(10):2179-93. Epub 2012 Aug 14.

Division of Environmental Health Sciences, Wadsworth Center, New York State Department of Health , Albany, New York 12201, USA.

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October 2012

QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation.

Anal Chem 2012 Jul 27;84(14):5845-50. Epub 2012 Jun 27.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, United States.

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July 2012

Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.

Anal Bioanal Chem 2012 Sep 3;404(4):1115-25. Epub 2012 May 3.

Department of Biomedical Informatics, Vanderbilt University Medical School, Nashville, TN 37232-8575, USA.

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September 2012

Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.

Curr Protoc Bioinformatics 2012 Mar;Chapter 13:Unit13.17

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.

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March 2012

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.

J Proteome Res 2012 Mar 27;11(3):1686-95. Epub 2012 Jan 27.

Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee 37232-8575, United States.

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March 2012

Protein identification using customized protein sequence databases derived from RNA-Seq data.

J Proteome Res 2012 Feb 14;11(2):1009-17. Epub 2011 Dec 14.

Department of Biomedical Informatics,Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States.

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February 2012

Supporting tool suite for production proteomics.

Bioinformatics 2011 Nov 29;27(22):3214-5. Epub 2011 Sep 29.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

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November 2011

A face in the crowd: recognizing peptides through database search.

Mol Cell Proteomics 2011 Nov 29;10(11):R111.009522. Epub 2011 Aug 29.

University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA.

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November 2011

ScanRanker: Quality assessment of tandem mass spectra via sequence tagging.

J Proteome Res 2011 Jul 26;10(7):2896-904. Epub 2011 Apr 26.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8340, USA.

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July 2011

A bioinformatics workflow for variant peptide detection in shotgun proteomics.

Mol Cell Proteomics 2011 May 9;10(5):M110.006536. Epub 2011 Mar 9.

Department of Biomedical Informatics,Vanderbilt University School of Medicine, 2525 West End Ave, Suite 800, Nashville, TN 37232, USA.

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May 2011

Proteomic analysis of the enterocyte brush border.

Am J Physiol Gastrointest Liver Physiol 2011 May 17;300(5):G914-26. Epub 2011 Feb 17.

Dept. of Cell and Developmental Biology, Vanderbilt Univ. Medical Center, Nashville, TN 37232, USA.

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May 2011

Sequence tagging reveals unexpected modifications in toxicoproteomics.

Chem Res Toxicol 2011 Feb 7;24(2):204-16. Epub 2011 Jan 7.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0006, United States.

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February 2011

TagRecon: high-throughput mutation identification through sequence tagging.

J Proteome Res 2010 Apr;9(4):1716-26

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8340, USA.

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April 2010

Identification and validation of novel spinophilin-associated proteins in rodent striatum using an enhanced ex vivo shotgun proteomics approach.

Mol Cell Proteomics 2010 Jun 2;9(6):1243-59. Epub 2010 Feb 2.

Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232-0615, USA.

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June 2010

Differential localization and dynamics of class I myosins in the enterocyte microvillus.

Mol Biol Cell 2010 Mar 20;21(6):970-8. Epub 2010 Jan 20.

Cell and Developmental Biology Department, Vanderbilt University School of Medicine, Nashville, TN 37205, USA.

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March 2010

Network-assisted protein identification and data interpretation in shotgun proteomics.

Mol Syst Biol 2009 18;5:303. Epub 2009 Aug 18.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232-8340, USA.

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November 2009

The enterocyte microvillus is a vesicle-generating organelle.

J Cell Biol 2009 Jun;185(7):1285-98

Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

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June 2009

The bis-electrophile diepoxybutane cross-links DNA to human histones but does not result in enhanced mutagenesis in recombinant systems.

Chem Res Toxicol 2009 Jun;22(6):1069-76

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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June 2009

Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

J Proteome Res 2008 Dec;7(12):5286-94

Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232, USA.

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December 2008

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.

J Proteome Res 2008 Sep 17;7(9):3838-46. Epub 2008 Jul 17.

Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, USA.

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September 2008

A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism.

Mol Cell Proteomics 2008 Nov 2;7(11):2090-106. Epub 2008 Jul 2.

Department of Molecular Physiology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615, USA.

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November 2008

Validation of tandem mass spectrometry database search results using DTASelect.

Curr Protoc Bioinformatics 2007 Jan;Chapter 13:Unit 13.4

The Scripps Research Institute, La Jolla, California, USA.

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January 2007

What's driving false discovery rates?

Authors:
David L Tabb

J Proteome Res 2008 Jan 15;7(1):45-6. Epub 2007 Dec 15.

Department of Biomedical Informatics and Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, USA.

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January 2008

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency.

J Proteome Res 2007 Sep 4;6(9):3549-57. Epub 2007 Aug 4.

Department of Biomedical Informatics, Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, USA.

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September 2007

Verification of automated peptide identifications from proteomic tandem mass spectra.

Nat Protoc 2006 ;1(5):2213-22

Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8340, USA.

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October 2007

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.

J Proteome Res 2007 Feb;6(2):654-61

Mass Spectrometry Research Center / Departments of Biomedical Informatics and Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232-8575, USA.

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February 2007

ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation.

Anal Chem 2006 Oct;78(20):7121-31

Chemical Sciences Division, Computational Biology Institute, Genome Science and Technology Graduate School, Oak Ridge National Laboratory-University of Tennessee, Oak Ridge, Tennessee 37830, USA.

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October 2006

Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics.

Anal Chem 2006 Oct;78(20):7110-20

Computational Biology Institute, Chemical Sciences Division, Oak Ridge National Laboratory-University of Tennessee, Oak Ridge, Tennessee 37830, USA.

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October 2006

Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra.

J Am Soc Mass Spectrom 2006 Jul 19;17(7):903-915. Epub 2006 May 19.

Chemical Sciences Division, Oak Ridge National Laboratory, MS 6131, P.O. Box 2008, 37831-6131, Oak Ridge, TN, USA.

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July 2006

Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems.

Anal Chem 2006 Jan;78(1):125-34

Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.

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January 2006

MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence.

Anal Chem 2005 Dec;77(23):7581-93

Graduate School of Genome Science and Technology, University of Tennessee--Oak Ridge National Laboratory, 37830-8026, USA.

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December 2005

MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

J Am Soc Mass Spectrom 2005 Aug;16(8):1250-61

Life Sciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee 37831, USA.

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August 2005

DBDigger: reorganized proteomic database identification that improves flexibility and speed.

Anal Chem 2005 Apr;77(8):2464-74

Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6164, USA.

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April 2005

Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.

Anal Chem 2004 Mar;76(5):1243-8

SR11 Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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March 2004

Automated discrimination of polymerase chain reaction products with closely related sequences by software-based detection of characteristic peaks in product ion spectra.

Rapid Commun Mass Spectrom 2003 ;17(24):2755-62

Department of Pathology and Microbiology, University of South Carolina School of Medicine, Columbia, SC 29209, USA.

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April 2004