| 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 | 4887 | 2010 |
| 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 | 3657 | 2012 |
| 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 | 1002 | 2014 |
| 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 | 737 | 2020 |
| 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 | 665 | 2020 |
| 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 | 654 | 2012 |
| 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 | 583 | 2014 |
| 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 | 507 | 2012 |
| 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 | 493 | 2018 |
| The ProteomeXchange consortium at 10 years: 2023 update EW Deutsch, N Bandeira, Y Perez-Riverol, V Sharma, JJ Carver, ... Nucleic acids research 51 (D1), D1539-D1548, 2023 | 397 | 2023 |
| 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 | 372 | 2020 |
| 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 | 368 | 2015 |
| 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 | 360 | 2013 |
| 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 | 351 | 2016 |
| 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 | 276 | 2010 |
| 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 | 249 | 2015 |
| 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 | 236 | 2006 |
| 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 | 227 | 2014 |
| 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 | 225 | 2017 |
| Panorama public: a public repository for quantitative data sets processed in skyline V Sharma, J Eckels, B Schilling, C Ludwig, JD Jaffe, MJ MacCoss, ... Molecular & Cellular Proteomics 17 (6), 1239-1244, 2018 | 219 | 2018 |