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Brendan MacLean
Brendan MacLean
Verified email at uw.edu
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Year
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
B MacLean, DM Tomazela, N Shulman, M Chambers, GL Finney, ...
Bioinformatics 26 (7), 966-968, 2010
44632010
A cross-platform toolkit for mass spectrometry and proteomics
MC Chambers, B Maclean, R Burke, D Amodei, DL Ruderman, ...
Nature biotechnology 30 (10), 918-920, 2012
30882012
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
M Choi, CY Chang, T Clough, D Broudy, T Killeen, B MacLean, O Vitek
Bioinformatics 30 (17), 2524-2526, 2014
8832014
The ProteomeXchange consortium in 2020: enabling ‘big data’approaches in proteomics
EW Deutsch, N Bandeira, V Sharma, Y Perez-Riverol, JJ Carver, ...
Nucleic acids research 48 (D1), D1145-D1152, 2020
6422020
Using i RT, a normalized retention time for more targeted measurement of peptides
C Escher, L Reiter, B MacLean, R Ossola, F Herzog, J Chilton, ...
Proteomics 12 (8), 1111-1121, 2012
6052012
Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach
SA Carr, SE Abbatiello, BL Ackermann, C Borchers, B Domon, ...
Molecular & Cellular Proteomics 13 (3), 907-917, 2014
5522014
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics
LK Pino, BC Searle, JG Bollinger, B Nunn, B MacLean, MJ MacCoss
Mass spectrometry reviews 39 (3), 229-244, 2020
5212020
Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation
B Schilling, MJ Rardin, BX MacLean, AM Zawadzka, BE Frewen, ...
Molecular & Cellular Proteomics 11 (5), 202-214, 2012
4862012
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
BC Searle, LK Pino, JD Egertson, YS Ting, RT Lawrence, BX MacLean, ...
Nature communications 9 (1), 5128, 2018
3692018
Building high-quality assay libraries for targeted analysis of SWATH MS data
OT Schubert, LC Gillet, BC Collins, P Navarro, G Rosenberger, WE Wolski, ...
Nature protocols 10 (3), 426-441, 2015
3442015
Multiplexed MS/MS for improved data-independent acquisition
JD Egertson, A Kuehn, GE Merrihew, NW Bateman, BX MacLean, YS Ting, ...
Nature methods 10 (8), 744-746, 2013
3392013
A multicenter study benchmarks software tools for label-free proteome quantification
P Navarro, J Kuharev, LC Gillet, OM Bernhardt, B MacLean, HL Röst, ...
Nature biotechnology 34 (11), 1130-1136, 2016
3252016
Skyline for small molecules: a unifying software package for quantitative metabolomics
KJ Adams, B Pratt, N Bose, LG Dubois, L St. John-Williams, KM Perrott, ...
Journal of proteome research 19 (4), 1447-1458, 2020
2792020
Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry
B MacLean, DM Tomazela, SE Abbatiello, S Zhang, JR Whiteaker, ...
Analytical chemistry 82 (24), 10116-10124, 2010
2632010
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
B MacLean, JK Eng, RC Beavis, M McIntosh
Bioinformatics 22 (22), 2830-2832, 2006
2342006
Multiplexed peptide analysis using data-independent acquisition and Skyline
JD Egertson, B MacLean, R Johnson, Y Xuan, MJ MacCoss
Nature protocols 10 (6), 887-903, 2015
2202015
Panorama: a targeted proteomics knowledge base
V Sharma, J Eckels, GK Taylor, NJ Shulman, AB Stergachis, SA Joyner, ...
Journal of proteome research 13 (9), 4205-4210, 2014
2152014
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
G Rosenberger, I Bludau, U Schmitt, M Heusel, CL Hunter, Y Liu, ...
Nature methods 14 (9), 921-927, 2017
2072017
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments
A Rauch, M Bellew, J Eng, M Fitzgibbon, T Holzman, P Hussey, M Igra, ...
Journal of proteome research 5 (1), 112-121, 2006
2022006
Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma
SE Abbatiello, B Schilling, DR Mani, LJ Zimmerman, SC Hall, B MacLean, ...
Molecular & Cellular Proteomics 14 (9), 2357-2374, 2015
1912015
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