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Author Details

Ben C Collins
Queen's University of Belfast
2007
52
28
PMIDPaper TitleJournal TitlePublished Year
37058003Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.J Proteome Res2023
34189564The protein landscape of chronic lymphocytic leukemia.Blood2021
33687722System-Wide Profiling of Protein Complexes Via Size Exclusion Chromatography-Mass Spectrometry (SEC-MS).Methods Mol Biol2021
34432947Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial.Mol Syst Biol2021
34798055Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation.Mol Cell2021
34155216Systematic detection of functional proteoform groups from bottom-up proteomic datasets.Nat Commun2021
34032011From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions.Mol Syst Biol2021
34228548Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance.Antimicrob Agents Chemother2021
32690956Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes.Nat Protoc2020
32027860A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS.Cell Syst2020
32094660Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.Nat Biotechnol2020
33257825diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition.Nat Methods2020
33333029SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles.Cell Syst2020
31175306Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.Nat Commun2019
29599191AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation.Mol Cell Proteomics2018
30104418Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.Mol Syst Biol2018
30412198Proteomics goes parallel.Nat Biotechnol2018
28604659Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.Nat Biotechnol2017
28223351<i>In Vivo</i> and <i>in Vitro</i> Proteome Analysis of Human Immunodeficiency Virus (HIV)-1-infected, Human CD4<sup>+</sup> T Cells.Mol Cell Proteomics2017
28355572Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry.Cell Rep2017
29032348Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis.Curr Opin Microbiol2017
28811595Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival.Sci Rep2017
28569762Quantitative proteomics: challenges and opportunities in basic and applied research.Nat Protoc2017
28806587Elucidation of host-pathogen protein-protein interactions to uncover mechanisms of host cell rewiring.Curr Opin Microbiol2017
28748474Absolute Quantification of Toxicological Biomarkers via Mass Spectrometry.Methods Mol Biol2017
28827567Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.Nat Commun2017
28825704Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.Nat Methods2017
27542680Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH.Proteomics2016
28725473Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen <i>Enterococcus faecalis</i>.NPJ Syst Biol Appl2016
27479329TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.Nat Methods2016
25730263Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.Nat Med2015
26381204mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.J Proteomics2015
26121405Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.Nat Methods2015
26094805Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.Cell Host Microbe2015
26199342Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.Mol Cell Proteomics2015
25652787Quantitative variability of 342 plasma proteins in a human twin population.Mol Syst Biol2015
25675208Building high-quality assay libraries for targeted analysis of SWATH MS data.Nat Protoc2015
24727770OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.Nat Biotechnol2014
25977788A repository of assays to quantify 10,000 human proteins by SWATH-MS.Sci Data2014
24741114Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.Mol Cell Proteomics2014
24162925Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.Nat Methods2013
24138574Mass spectrometric protein maps for biomarker discovery and clinical research.Expert Rev Mol Diagn2013
22577020Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate.Proteomics2012
22807453Focus on cancer proteomics.Proteomics2012
22527513Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach.Mol Cell Proteomics2012
20972766Differential proteomics incorporating iTRAQ labeling and multi-dimensional separations.Methods Mol Biol2011
22005152Serum proteomic profiling reveals that pretreatment complement protein levels are predictive of esophageal cancer patient response to neoadjuvant chemoradiation.Ann Surg2011
21214251Sequence tagging reveals unexpected modifications in toxicoproteomics.Chem Res Toxicol2011
20972768Absolute quantification of toxicological biomarkers by multiple reaction monitoring.Methods Mol Biol2011
20162557Use of SELDI MS to discover and identify potential biomarkers of toxicity in InnoMed PredTox: a multi-site, multi-compound study.Proteomics2010
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Collaborators

Ruedi Aebersold
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 40
Yansheng Liu
Yale University School of Medicine
Co-authored papers 11
Ludovic Gillet
ETH Zurich
Co-authored papers 11
William M Gallagher
All-Island Cancer Research Institute, UCD Conway Institute, University College Dublin
Co-authored papers 9
Moritz Heusel
Lund University
Co-authored papers 8
Stephen R Pennington
UCD Conway Institute, University College Dublin
Co-authored papers 7
Matthias Gstaiger
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 7
Isabell Bludau
Max-Planck Institute of Biochemistry
Co-authored papers 7
Anne-Claude Gingras
Lunenfeld-Tanenbaum Research Institute
Co-authored papers 3
Claudia Martelli
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 3
Fabian Frommelt
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 3
Tiannan Guo
Westlake University
Co-authored papers 3
Patrick G A Pedrioli
Institute of Translational Medicine, Swiss Federal Institute of Technology/ETH Zurich
Co-authored papers 3
Charlotte Nicod
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 3
Emmanouil T Dermitzakis
University of Geneva
Co-authored papers 2
Andrea Fossati
J. David Gladstone Institutes
Co-authored papers 2
Federico Uliana
Institute of Biochemistry, ETH Zurich
Co-authored papers 2
Alexey I Nesvizhskii
University of Michigan ann arbor
Co-authored papers 2
Christie L Hunter
Co-authored papers 2
Brendan MacLean
Co-authored papers 2
Ruth H??ttenhain
Quantitative Biosciences Institute (QBI), University of California san francisco
Co-authored papers 2
Bernd Wollscheid
ETH Zurich
Co-authored papers 2
Evan G Williams
University of Luxembourg
Co-authored papers 2
Tim D Spector
King's College London
Co-authored papers 2
Robert L Moritz
Institute for Systems Biology
Co-authored papers 2
Gunnar R??tsch
ETH Zurich
Co-authored papers 1
Sandra Goetze
ETH Zurich
Co-authored papers 1
Wenguang Shao
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1
Birgit Schilling
Buck Institute for Research on Aging
Co-authored papers 1
Wolfgang Huber
Technische Universitat Munchen
Co-authored papers 1
Release 1.2