Author details

Full Name

Brendan MacLean

Affiliation

ORCID

Career Start Year

2006

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37533638	Targeted proteomics data interpretation with DeepMRM.		2023
36370099	The ProteomeXchange consortium at 10 years: 2023 update.	Nucleic Acids Res	2023
36165806	TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies.	J Proteome Res	2023
37694881	Localization and Quantification of Post-Translational Modifications of Proteins Using Electron Activated Dissociation Fragmentation on a Fast-Acquisition Time-of-Flight Mass Spectrometer.	J Am Soc Mass Spectrom	2023
37398334	Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition.	bioRxiv	2023
37018319	MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.	J Proteome Res	2023
34919405	Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline.	J Proteome Res	2022
35831612	Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions.	Nat Protoc	2022
35716664	Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain.	Structure	2022
28691345	The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.	Mass Spectrom Rev	2020
31686107	The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.	Nucleic Acids Res	2020
32234965	Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments.	Mol Cell Proteomics	2020
32345972	LipidCreator workbench to probe the lipidomic landscape.	Nat Commun	2020
31984744	Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.	J Proteome Res	2020
32467974	Audit logs to enforce document integrity in Skyline and Panorama.	Bioinformatics	2020
33199889	Avant-garde: an automated data-driven DIA data curation tool.	Nat Methods	2020
30671891	Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.	J Am Soc Mass Spectrom	2019
31065629	Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping.	Analyst	2019
29203474	Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin.	Clin Chem	2018
30510204	Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.	Nat Commun	2018
30047074	Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions.	J Am Soc Mass Spectrom	2018
29487113	Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.	Mol Cell Proteomics	2018
29655704	A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.	Cell Syst	2018
27990823	ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.	J Proteome Res	2017
28825704	Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.	Nat Methods	2017
28483925	MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments.	Mol Cell Proteomics	2017
28183812	New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.	Mol Cell Proteomics	2017
27700092	An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments.	J Proteome Res	2016
26867747	Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.	Methods Mol Biol	2016
27701404	A multicenter study benchmarks software tools for label-free proteome quantification.	Nat Biotechnol	2016
25987414	MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.	Mol Cell Proteomics	2015
25693799	Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.	Mol Cell Proteomics	2015
25675208	Building high-quality assay libraries for targeted analysis of SWATH MS data.	Nat Protoc	2015
26398777	Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows.	Anal Chem	2015
26217018	Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.	Mol Cell Proteomics	2015
25996789	Multiplexed peptide analysis using data-independent acquisition and Skyline.	Nat Protoc	2015
25102069	Panorama: a targeted proteomics knowledge base.	J Proteome Res	2014
24443746	Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.	Mol Cell Proteomics	2014
24496601	Implementation of statistical process control for proteomic experiments via LC MS/MS.	J Am Soc Mass Spectrom	2014
24320210	Accounting for population variation in targeted proteomics.	J Proteome Res	2014
24813211	A framework for installable external tools in Skyline.	Bioinformatics	2014
24794931	MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.	Bioinformatics	2014
24972168	CPTAC Assay Portal: a repository of targeted proteomic assays.	Nat Methods	2014
23689285	Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).	Mol Cell Proteomics	2013
23793237	Multiplexed MS/MS for improved data-independent acquisition.	Nat Methods	2013
23051804	A cross-platform toolkit for mass spectrometry and proteomics.	Nat Biotechnol	2012
22577014	The development of selected reaction monitoring methods for targeted proteomics via empirical refinement.	Proteomics	2012
22577012	Using iRT, a normalized retention time for more targeted measurement of peptides.	Proteomics	2012
22454539	Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.	Mol Cell Proteomics	2012
22559222	Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides.	J Proteome Res	2012