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List of works by Jimmy K. Eng

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

scientific article

A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry

scientific article published on February 2007

A common open representation of mass spectrometry data and its application to proteomics research

scientific article

A deeper look into Comet--implementation and features

scientific article published on 27 June 2015

A face in the crowd: recognizing peptides through database search

scientific article published on 29 August 2011

A fast SEQUEST cross correlation algorithm

scientific article published on 6 September 2008

A guided tour of the Trans-Proteomic Pipeline

scientific article

A mass spectrometry proteomics data management platform

scientific article (publication date: September 2012)

A multidimensional chromatography technology for in-depth phosphoproteome analysis

scientific article published on 11 April 2008

A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies

scientific article published on May 2010

A platform for accurate mass and time analyses of mass spectrometry data

scientific article

A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.

scientific article published on 9 June 2006

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry

scientific article

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

scientific article

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification

scientific article published on 21 February 2012

An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experiments

scientific article published in January 2005

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

scientific article (publication date: November 1994)

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

scientific article published on August 2005

An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells

scientific article published on 19 February 2007

Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics

scientific article published on August 2009

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

scientific article published on January 2006

Androgen-sensitive microsomal signaling networks coupled to the proliferation and differentiation of human prostate cancer cells

scientific article published on October 2011

Building consensus spectral libraries for peptide identification in proteomics

scientific article

Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study

scientific article

Characterization of proteome of human cerebrospinal fluid

scientific article published in January 2006

Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry

scientific article

ChromEval: a software application for the rapid evaluation of HPLC system performance in proteomic applications.

scientific article published on June 2010

Code developments to improve the efficiency of automated MS/MS spectra interpretation

scientific article published in May 2002

Comet: an open-source MS/MS sequence database search tool

scientific article

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

scientific article published in April 2002

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

scientific article

Cross-linking measurements of in vivo protein complex topologies

scientific article

Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions

scientific article

Crux: rapid open source protein tandem mass spectrometry analysis

scientific article published on 9 September 2014

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics

scientific article

Development and validation of a spectral library searching method for peptide identification from MS/MS.

scientific article published in March 2007

Differential protein expression profiles in estrogen receptor-positive and -negative breast cancer tissues using label-free quantitative proteomics

scientific article

Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment

scientific article published on 27 May 2015

Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins ⬇️

scientific article published on October 1, 1997

Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format

scientific article published on 27 February 2020

Extracellular Matrix Proteins Mediate HIV-1 gp120 Interactions with α4β7.

scientific article published on 16 August 2017

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

scientific article

Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics

scientific article published on 06 April 2020

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine

scientific article published on 28 July 2006

Head-to-Head Comparison of Serum Fractionation Techniques

article

High throughput protein characterization by automated reverse‐phase chromatography/electrospray tandem mass spectrometry ⬇️

scientific article published on March 1, 1998

High throughput proteome screening for biomarker detection

scientific article published on 5 January 2005

Human Plasma PeptideAtlas

scientific article published on August 2005

Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry

scientific article

Identification of TFB5, a new component of general transcription and DNA repair factor IIH.

scientific article

Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells

scientific article

Identification of putative androgen receptor interaction protein modules: cytoskeleton and endosomes modulate androgen receptor signaling in prostate cancer cells

scientific article published on 18 October 2006

In vivo application of photocleavable protein interaction reporter technology

scientific article

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075

scientific article (publication date: 11 November 2016)

In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy

scientific article published on 28 February 2013

Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures

scientific article

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

scientific article

Installation and use of LabKey Server for proteomics

scientific article published on December 2011

Installation and use of the Computational Proteomics Analysis System (CPAS).

scientific article published on June 2007

Integrated genomic and proteomic analyses of gene expression in Mammalian cells

scientific article published on 6 July 2004

Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer

scientific article published on 21 August 2007

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

scientific article

Investigation of neutral loss during collision-induced dissociation of peptide ions

scientific article

In Vivo Conformational Dynamics of Hsp90 and Its Interactors

scientific article published on June 2016

Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers

scientific article published on 30 November 2016

Lipid raft proteins and their identification in T lymphocytes.

scientific article published in January 2004

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments

scientific article

MaRiMba: a software application for spectral library-based MRM transition list assembly

scientific article

Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.

scientific article

Method To Compare Collision-Induced Dissociation Spectra of Peptides: Potential for Library Searching and Subtractive Analysis ⬇️

scientific article published on September 1, 1998

Microdialysis combined with proteomics for protein identification in breast tumor microenvironment in vivo

scientific article

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

scientific article published in August 2005

PROTEOME-3D: an interactive bioinformatics tool for large-scale data exploration and knowledge discovery

scientific article

Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape

scientific article published on October 2005

Precursor charge state prediction for electron transfer dissociation tandem mass spectra

scientific article published on October 2010

Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry

scientific article published on 19 March 2015

Protein Identification by SEQUEST

article

Protein identification using TurboSEQUEST.

scientific article published in July 2005

Protein interactions, post-translational modifications and topologies in human cells

scientific article

Protein kinase PKN1 represses Wnt/β-catenin signaling in human melanoma cells

scientific article published on 10 October 2013

Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags

scientific article

Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.

scientific article

Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry

scientific article published in July 2005

Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli

scientific article published on 26 February 2004

Proteomics analysis of human coronary atherosclerotic plaque: a feasibility study of direct tissue proteomics by liquid chromatography and tandem mass spectrometry

scientific article published on 5 March 2007

Proteomics data repositories

scientific article published in October 2009

Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles

scientific article published in July 2006

Quantification of the compositional information provided by immonium ions on a quadrupole-time-of-flight mass spectrometer

scientific article published on 20 June 2008

Quantitative Proteomics Based on Optimized Data-Independent Acquisition in Plasma Analysis.

scientific article

Quantitative analysis of the secretome of TGF-beta signaling-deficient mammary fibroblasts

scientific article

Quantitative interactome analysis reveals a chemoresistant edgotype

scientific article

Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry

scientific article

Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions

scientific article

Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways

scholarly article

Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid

scientific article published in February 2005

Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease

scientific article published in April 2005

Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks

scientific article published on 16 July 2015

Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides

scientific article published in November 1996

Sipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics

scientific article published on 22 September 2017

Sites of ubiquitin attachment in Saccharomyces cerevisiae

scientific article published on 20 December 2011

Spectral Library Searching To Identify Cross-Linked Peptides

scientific article

System-based proteomic analysis of the interferon response in human liver cells

scientific article

Systematic characterization of nuclear proteome during apoptosis: a quantitative proteomic study by differential extraction and stable isotope labeling

scientific article published on 14 March 2006

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

scientific article published on 6 February 2013

Systemic Proteome Alterations Linked to Early Stage Pancreatic Cancer in Diabetic Patients

scientific article published on 11 June 2020

The PeptideAtlas project

scientific article

The Pseudomonas aeruginosa proteome during anaerobic growth

scientific article

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT

scientific article published on 25 June 2003

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the applicatio

scientific article

The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching

scientific article

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

scientific article

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

scientific article

UniPep--a database for human N-linked glycosites: a resource for biomarker discovery

scientific article published on 10 August 2006

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

scientific article published on 9 December 2015

XLink-DB: database and software tools for storing and visualizing protein interaction topology data

scientific article

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

scientific article

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates

scientific article

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