Search filters

List of works by David Tabb

A Laboratory-Targeted, Data Management and Processing System for the Early Detection Research Network

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

scientific article published on 13 April 2018

A bioinformatics workflow for variant peptide detection in shotgun proteomics

scientific article

A cross-platform toolkit for mass spectrometry and proteomics

scientific article

A face in the crowd: recognizing peptides through database search

scientific article published on 29 August 2011

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

scientific article published on 02 July 2008

A standardized framing for reporting protein identifications in mzIdentML 1.2

scientific article

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

scientific article

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

scientific article

Basophile: accurate fragment charge state prediction improves peptide identification rates

scientific article published on 08 March 2013

Bioinformatics and Database Searching

Bioinformatics of Proteomic Tandem Mass Spectra: Selection, Characterization, and Identification ⬇️

doctoral thesis by David L. Tabb, 2003

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

scientific article published on 23 March 2018

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

scientific article published on 01 January 2018

Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach

scientific article published in September 2004

Chronic intermittent alcohol disrupts the GluN2B-associated proteome and specifically regulates group I mGlu receptor-dependent long-term depression

scientific article published on 8 November 2015

Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra

scientific article

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

scientific article

Correcting systematic bias and instrument measurement drift with mzRefinery

scientific article

Corrigendum: Proteomic analysis of colon and rectal carcinoma using standard and customized databases

scientific article published on 21 July 2015

DBDigger: reorganized proteomic database identification that improves flexibility and speed

scientific article published in April 2005

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

scientific article (publication date: 2002)

Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states

scientific article published in February 2006

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

scientific article published on 19 May 2006

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

scientific journal article

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

scientific article

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

scientific article published on 01 December 2020

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

scientific article published in January 2006

Employing ProteoWizard to Convert Raw Mass Spectrometry Data

scientific article

Enabling proteomics-based identification of human cancer variations

scientific article published on 23 July 2010

Evaluating protein interactions through cross-linking mass spectrometry ⬇️

scientific article published on September 1, 2012

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

scientific article published on December 2008

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

scientific article

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model

scientific article published on December 2003

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions

scientific article published on 20 March 2013

Host blood RNA signatures predict the outcome of tuberculosis treatment.

scientific article published on 12 August 2017

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

scientific article published on 12 August 2013

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

scientific article

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

scientific article

Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry.

scientific article published on 18 September 2013

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

scientific article

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome

scientific article published on 22 March 2019

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

scientific article published on 4 August 2016

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

scientific article published on March 2004

Informatics of protein and posttranslational modification detection via shotgun proteomics

scientific article

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

scientific article published on 28 June 2016

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

scientific article

Large-scale protein identification using mass spectrometry

scientific article published in March 2003

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

scientific article published in December 2005

MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR Products

article

MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.

scientific article published on January 2004

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

scientific article published in August 2005

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

scientific article

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma

scientific article

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

scientific article

Network-assisted protein identification and data interpretation in shotgun proteomics

scientific article

Neurovascular unit on a chip: implications for translational applications.

scientific article

Obesity and altered glucose metabolism impact HDL composition in CETP transgenic mice: a role for ovarian hormones.

scientific article published on 3 January 2012

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

scientific article

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses

scientific article

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

scientific article published in October 2006

Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes

scientific article

Protein Identification by SEQUEST

article

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

scientific article

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates

scientific article published on 18 August 2017

Proteogenomic characterization of human colon and rectal cancer

scientific article (publication date: 18 September 2014)

Proteomic analysis of Chinese hamster ovary cells

scientific article published on 05 October 2012

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

scientific article published on 23 June 2015

Proteomic analysis of the enterocyte brush border

scientific article

Proteomic analysis reveals that sulfamethoxazole induces oxidative stress in M. tuberculosis

scientific article published on 17 May 2018

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

scientific article

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

scientific article

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

scientific article published on 27 June 2012

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.

scientific article published on 10 November 2017

Quality assessment for clinical proteomics ⬇️

scientific article published on December 12, 2012

Quality control in mass spectrometry-based proteomics

scientific article published on 12 August 2017

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

scientific article

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)

scientific article

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

scientific article published on 3 November 2011

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

scientific article published on 14 December 2011

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

scientific article published in December 2011

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

scientific article published on 03 May 2012

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry

scientific article

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

scientific article published on 14 December 2015

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

scientific article published in October 2006

ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging.

scientific article

ScanRanker: Quality assessment of tandem mass spectra via sequence tagging

scientific article published on 26 April 2011

Sequence tagging reveals unexpected modifications in toxicoproteomics

scientific article published on 7 January 2011

Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility

scientific article published in May 2003

Sipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics

scientific article published on 22 September 2017

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

scientific article

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

scientific article published on 9 February 2010

Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides

scientific article

Supporting tool suite for production proteomics

scientific article published on 29 September 2011

TagRecon: high-throughput mutation identification through sequence tagging

scientific article

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences

scientific article

Technologies for Large-Scale Proteomic Tandem Mass Spectrometry

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses

scientific article published on 4 October 2015

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

scientific article

The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

The SEQUEST family tree

scientific article

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

scientific article published on June 2009

The enterocyte microvillus is a vesicle-generating organelle

scientific article

The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae.

scientific article

The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides

article

Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis

scientific article

Validation of tandem mass spectrometry database search results using DTASelect

scientific article published on January 2007

Verification of automated peptide identifications from proteomic tandem mass spectra

scientific article

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

scientific article

What's driving false discovery rates?

scientific article published on 15 December 2007

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

scientific article

Paulina is supported by:

About Paulina

Help