| A guided tour of the Trans‐Proteomic Pipeline EW Deutsch, L Mendoza, D Shteynberg, T Farrah, H Lam, N Tasman, ... Proteomics 10 (6), 1150-1159, 2010 | 860 | 2010 |
| iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates D Shteynberg, EW Deutsch, H Lam, JK Eng, Z Sun, N Tasman, ... Molecular & cellular proteomics 10 (12), 2011 | 617 | 2011 |
| Trans‐Proteomic Pipeline, a standardized data processing pipeline for large‐scale reproducible proteomics informatics EW Deutsch, L Mendoza, D Shteynberg, J Slagel, Z Sun, RL Moritz PROTEOMICS–Clinical Applications 9 (7-8), 745-754, 2015 | 350 | 2015 |
| 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 | 338 | 2023 |
| PASSEL: The P eptide A tlas SRM experiment library T Farrah, EW Deutsch, R Kreisberg, Z Sun, DS Campbell, L Mendoza, ... Proteomics 12 (8), 1170-1175, 2012 | 240 | 2012 |
| PTMProphet: Fast and accurate mass modification localization for the trans-proteomic pipeline DD Shteynberg, EW Deutsch, DS Campbell, MR Hoopmann, ... Journal of proteome research 18 (12), 4262-4272, 2019 | 111 | 2019 |
| Formulation and in Vitro, ex Vivo and in Vivo Evaluation of Elastic Liposomes for Transdermal Delivery of Ketorolac Tromethamine G Nava, E Piñón, L Mendoza, N Mendoza, D Quintanar, A Ganem Pharmaceutics 3 (4), 954-970, 2011 | 100 | 2011 |
| Potential effect of probiotics in the treatment of breast cancer L Mendoza Oncology reviews 13 (2), 2019 | 88 | 2019 |
| MaRiMba: a software application for spectral library-based MRM transition list assembly CA Sherwood, A Eastham, LW Lee, A Peterson, JK Eng, D Shteynberg, ... Journal of proteome research 8 (10), 4396-4405, 2009 | 85 | 2009 |
| TraML—a standard format for exchange of selected reaction monitoring transition lists EW Deutsch, M Chambers, S Neumann, F Levander, PA Binz, J Shofstahl, ... Molecular & Cellular Proteomics 11 (4), 2012 | 84 | 2012 |
| State of the human proteome in 2014/2015 as viewed through PeptideAtlas: enhancing accuracy and coverage through the AtlasProphet EW Deutsch, Z Sun, D Campbell, U Kusebauch, CS Chu, L Mendoza, ... Journal of proteome research 14 (9), 3461-3473, 2015 | 77 | 2015 |
| Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science DR Unni, SAT Moxon, M Bada, M Brush, R Bruskiewich, JH Caufield, ... Clinical and translational science 15 (8), 1848-1855, 2022 | 64 | 2022 |
| Universal Spectrum Identifier for mass spectra EW Deutsch, Y Perez-Riverol, J Carver, S Kawano, L Mendoza, ... Nature methods 18 (7), 768-770, 2021 | 64 | 2021 |
| Expanding the use of spectral libraries in proteomics EW Deutsch, Y Perez-Riverol, RJ Chalkley, M Wilhelm, S Tate, ... Journal of proteome research 17 (12), 4051-4060, 2018 | 64 | 2018 |
| Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin J Millan-Onate, W Millan, LA Mendoza, CG Sánchez, ... Annals of Clinical Microbiology and Antimicrobials 19, 1-9, 2020 | 59 | 2020 |
| Trans-proteomic pipeline: robust mass spectrometry-based proteomics data analysis suite EW Deutsch, L Mendoza, DD Shteynberg, MR Hoopmann, Z Sun, JK Eng, ... Journal of proteome research 22 (2), 615-624, 2023 | 50 | 2023 |
| The Arabidopsis PeptideAtlas: harnessing worldwide proteomics data to create a comprehensive community proteomics resource KJ Van Wijk, T Leppert, Q Sun, SS Boguraev, Z Sun, L Mendoza, ... The Plant Cell 33 (11), 3421-3453, 2021 | 46 | 2021 |
| Trans‐Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets EW Deutsch, D Shteynberg, H Lam, Z Sun, JK Eng, C Carapito, ... Proteomics 10 (6), 1190-1195, 2010 | 43 | 2010 |
| Interleukin-2 and dendritic cells as adjuvants for surgical therapy of tumours associated with human papillomavirus type 16 J Bubenı́k, R Mikyšková, V Vonka, L Mendoza, J Šı́mová, M Šmahel, ... Vaccine 21 (9-10), 891-896, 2003 | 39 | 2003 |
| The microvesicle component of HIV-1 inocula modulates dendritic cell infection and maturation and enhances adhesion to and activation of T lymphocytes SK Mercier, H Donaghy, RA Botting, SG Turville, AN Harman, N Nasr, H Ji, ... PLoS pathogens 9 (10), e1003700, 2013 | 36 | 2013 |
