|OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data|
HL Röst, G Rosenberger, P Navarro, L Gillet, SM Miladinović, ...
Nature biotechnology 32 (3), 219, 2014
|Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system|
BC Collins, LC Gillet, G Rosenberger, HL Röst, A Vichalkovski, ...
Nature methods 10 (12), 1246, 2013
|A repository of assays to quantify 10,000 human proteins by SWATH-MS|
G Rosenberger, CC Koh, T Guo, HL Röst, P Kouvonen, BC Collins, ...
Scientific data 1, 140031, 2014
|Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps|
T Guo, P Kouvonen, CC Koh, LC Gillet, WE Wolski, HL Röst, ...
Nature medicine 21 (4), 407-413, 2015
|Quantitative variability of 342 plasma proteins in a human twin population|
Y Liu, A Buil, BC Collins, LCJ Gillet, LC Blum, LY Cheng, O Vitek, ...
Molecular systems biology 11 (2), 2015
|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, 2015
|Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry|
BC Collins, CL Hunter, Y Liu, B Schilling, G Rosenberger, SL Bader, ...
Nature communications 8 (1), 1-12, 2017
|Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor …|
Y Liu, J Chen, A Sethi, QK Li, L Chen, B Collins, LCJ Gillet, B Wollscheid, ...
Molecular & Cellular Proteomics 13 (7), 1753-1768, 2014
|Absolute proteome composition and dynamics during dormancy and resuscitation of Mycobacterium tuberculosis|
OT Schubert, C Ludwig, M Kogadeeva, M Zimmermann, G Rosenberger, ...
Cell host & microbe 18 (1), 96-108, 2015
|Mass spectrometric protein maps for biomarker discovery and clinical research|
Y Liu, R Huettenhain, B Collins, R Aebersold
Expert review of molecular diagnostics 13 (8), 811-825, 2013
|Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial|
C Ludwig, L Gillet, G Rosenberger, S Amon, BC Collins, R Aebersold
Molecular systems biology 14 (8), 2018
|Quantitative proteomics: challenges and opportunities in basic and applied research|
OT Schubert, HL Röst, BC Collins, G Rosenberger, R Aebersold
Nature protocols 12 (7), 1289, 2017
|TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics|
HL Röst, Y Liu, G D'Agostino, M Zanella, P Navarro, G Rosenberger, ...
Nature methods 13 (9), 777, 2016
|Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation|
E Marcon, H Jain, A Bhattacharya, H Guo, S Phanse, S Pu, G Byram, ...
Nature methods 12 (8), 725-731, 2015
|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
|mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry|
G Teo, S Kim, CC Tsou, B Collins, AC Gingras, AI Nesvizhskii, H Choi
Journal of proteomics 129, 108-120, 2015
|Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS|
G Rosenberger, Y Liu, HL Röst, C Ludwig, A Buil, A Bensimon, M Soste, ...
Nature biotechnology 35 (8), 781-788, 2017
|Identification of a set of conserved eukaryotic internal retention time standards for data-independent acquisition mass spectrometry|
SJ Parker, H Rost, G Rosenberger, BC Collins, L Malmström, D Amodei, ...
Molecular & Cellular Proteomics 14 (10), 2800-2813, 2015
|Serum proteomic profiling reveals that pretreatment complement protein levels are predictive of esophageal cancer patient response to neoadjuvant chemoradiation|
SG Maher, DT McDowell, BC Collins, C Muldoon, WM Gallagher, ...
Annals of surgery 254 (5), 809-817, 2011
|Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate|
HA Ebhardt, E Sabidó, R Hüttenhain, B Collins, R Aebersold
Proteomics 12 (8), 1185-1193, 2012