Publications by authors named "Jimmy Eng"

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C
Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.
Christopher D McGann, Erik J Bergstrom, Vagisha Sharma, Lilian R Heil, Qing Yu, Jimmy K Eng

J Proteome Res· July 2025

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Open-Source and FAIR Research Software for Proteomics.
Yasset Perez-Riverol, Wout Bittremieux, William S Noble, Lennart Martens, Aivett Bilbao, Chengxin Dai, Jimmy K Eng

J Proteome Res· May 2025

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The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie

J Proteome Res· February 2023

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Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.
Eric W Deutsch, Luis Mendoza, David D Shteynberg, Michael R Hoopmann, Zhi Sun, Jimmy K Eng

J Proteome Res· February 2023

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Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification.
Ian R Smith, Jimmy K Eng, Anthony S Barente, Alexander Hogrebe, Ariadna Llovet

Anal Chem· November 2022

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Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.
Jimmy K Eng, Eric W Deutsch

Proteomics· November 2020

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Systemic Proteome Alterations Linked to Early Stage Pancreatic Cancer in Diabetic Patients.
Hong Peng, Sheng Pan, Yuanqing Yan, Randall E Brand, Gloria M Petersen, Jimmy K Eng

Cancers (Basel)· June 2020

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Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics.
Devin K Schweppe, Jimmy K Eng, Qing Yu, Derek Bailey, Ramin Rad

J Proteome Res· May 2020

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In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes.
Xuefei Zhong, Xia Wu, Devin K Schweppe, Juan D Chavez, Martin Mathay, Jimmy K Eng

J Am Soc Mass Spectrom· February 2020

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Predictive proteomic signatures for response of pancreatic cancer patients receiving chemotherapy.
Hong Peng, Ru Chen, Teresa A Brentnall, Jimmy K Eng, Vincent J Picozzi, Sheng Pan

Clin Proteomics· July 2019

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In Vivo Proteome of Pseudomonas aeruginosa in Airways of Cystic Fibrosis Patients.
Xia Wu, Richard J Siehnel, Jayanthi Garudathri, Benjamin J Staudinger, Katherine B Hisert, Jimmy K Eng

J Proteome Res· June 2019

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Proteomics Standards Initiative Extended FASTA Format.
Pierre-Alain Binz, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J Chalkley, Jimmy K Eng

J Proteome Res· June 2019

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Tools for 3D Interactome Visualization.
Andrew Keller, Juan D Chavez, Jimmy K Eng, Zorian Thornton, James E Bruce

J Proteome Res· February 2019

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A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry.
Kristian E Swearingen, Jimmy K Eng, David Shteynberg, Vladimir Vigdorovich, Timothy A Springer

J Proteome Res· February 2019

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Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins.
See-Yeun Ting, Dustin E Bosch, Sarah M Mangiameli, Matthew C Radey, Shuo Huang, Jimmy K Eng

Cell· November 2018

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Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.
Jared P Mohr, Poorna Perumalla, Juan D Chavez, Jimmy K Eng, James E Bruce

Anal Chem· May 2018

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Sipros Ensemble improves database searching and filtering for complex metaproteomics.
Xuan Guo, Zhou Li, Qiuming Yao, Ryan S Mueller, Jimmy K Eng

Bioinformatics· March 2018

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Extracellular Matrix Proteins Mediate HIV-1 gp120 Interactions with αβ.
David Plotnik, Wenjin Guo, Brad Cleveland, Priska von Haller, Jimmy K Eng

J Virol· November 2017

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A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.
Juan D Chavez, Jimmy K Eng, Devin K Schweppe, Michelle Cilia, Keith Rivera

PLoS One· June 2017

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Quantitative Proteomics Based on Optimized Data-Independent Acquisition in Plasma Analysis.
Eslam N Nigjeh, Ru Chen, Randall E Brand, Gloria M Petersen, Suresh T Chari, Jimmy K Eng, Ziding Feng, Sheng Pan

J Proteome Res· February 2017

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Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers.
Xuefei Zhong, Arti T Navare, Juan D Chavez, Jimmy K Eng, Devin K Schweppe

J Proteome Res· February 2017

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In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.
Xia Wu, Juan D Chavez, Devin K Schweppe, Chunxiang Zheng, Chad R Weisbrod, Jimmy K Eng

Nat Commun· November 2016

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XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.
Devin K Schweppe, Chunxiang Zheng, Juan D Chavez, Arti T Navare, Xia Wu, Jimmy K Eng

Bioinformatics· September 2016

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In Vivo Conformational Dynamics of Hsp90 and Its Interactors.
Juan D Chavez, Devin K Schweppe, Jimmy K Eng, James E Bruce

Cell Chem Biol· June 2016

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Spectral Library Searching To Identify Cross-Linked Peptides.
Devin K Schweppe, Juan D Chavez, Arti T Navare, Xia Wu, Bianca Ruiz, Jimmy K Eng

J Proteome Res· May 2016

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