ProCan Publications

Proteomic-based stratification of prostate cancer patients. Qing Zhong, Rui Sun, Adel T Aref, Zainab Noor, Asim Anees, Yi Zhu, Natasha Lucas, Rebecca C Poulos, Mengge Lyu, Tiansheng Zhu, Guo-Bo Chen, Yingrui Wang, Xuan Ding, Dorothea Rutishauser, Niels J Rupp, Jan H Rueschoff, Cédric Poyet, Thomas Hermanns, Christian Fankhauser, María Rodríguez Martínez, Wenguang Shao, Marija Buljan, Janis Frederick Neumann, Andreas Beyer, Peter G Hains, Roger R Reddel, Phillip J Robinson, Ruedi Aebersold, Tiannan Guo, Peter J Wild Life Science Alliance. Dec 2023, 7 (2) e202302146; DOI: 10.26508/lsa.202302146
Heat 'n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour. Xavier D, Lucas N, Williams SG, Koh JMS, Ashman K, Loudon C, Reddel R, Hains PG, Robinson PJ. Anal Chem. 2024 Mar 1. doi: 10.1021/acs.analchem.3c04708. Epub ahead of print. PMID: 38427620.
Retrospective analysis of clinical characteristics and outcomes of patients with carcinoma of unknown primary from three tertiary centers in Australia. Boys EL, Gao B, Grimison P, Sutherland S, MacKenzie KL, Reddel RR, Liu J. Cancer Med. 2024 Mar;13(6):e7052. doi: 10.1002/cam4.7052. PMID: 38523552; PMCID: PMC10961596.
Proteomic insights into paediatric cancer: Unravelling molecular signatures and therapeutic opportunities. Padhye BD, Nawaz U, Hains PG, Reddel RR, Robinson PJ, Zhong Q, Poulos RC. Pediatr Blood Cancer. 2024;e30980. PMID: 38556739. DOI: 10.1002/pbc.30980
Quantitative proteomic studies addressing unmet clinical needs in sarcoma. Connolly, E., Grimison, P., Horvath, L., Robinson, P.J. and Reddel, R.R.: Frontiers Oncol. 2023. 13:1126736. doi: 10.3389/fonc.2023.1126736
Opportunities for pharmacoproteomics in biomarker discovery. Poulos, R. C., Cai, Z., Robinson, P. J., Reddel, R. R., Zhong, Q. (2022). TM. Proteomics. 2022 Sep 10;e2200031. doi: 10.1002/pmic.202200031. PMID: 36086888.

Clinical applications of mass spectrometry-based proteomics in cancer: Where are we? Boys, E. L, Liu, J., Robinson, P. J., Reddel, R. R. TM. Proteomics. 2022 Aug 15;e2200238. doi: 10.1002/pmic.202200238. PMID: 35968695.

Targeting brain cancer: A new drug is designed to hit an old target with increased precision. Reddel, R. R., Aref A. TM. Science. 2022 Jul 29;377(6605):467-468. doi: 10.1126/science.add4839. PMID: 35901132.

Pan-cancer proteomic map of 949 human cell lines. Gonçalves, E., Poulos, R. C., Cai, Z., Barthorpe, s., Manda, S. S., Lucas, N., Beck, A., Bucio-Noble, D., Dausmann, M., Hall C., Hecker, M., Koh, J., Lightfoot, H., Mahboob, S., Mali, I., Morris, J., Richardson, L., Seneviratne, A. J., Shepherd, R., Sykes, E., Thomas, F., Valentini, S., Williams, S. G., Wu, Y., Xavier, D., MacKenzie, K. L., Hains, P. G., Tully, B., Robinson, P. J., Zhong, Q., Garnett, M. J., Reddel, R. R. TM. Cancer Cell. 2022 Aug 8;40(8):835-849.e8. doi: 10.1016/j.ccell.2022.06.010. PMID: 35839778.

Machine learning for multi-omics data integration in cancer. Cai, Z., Poulos, R. C., Liu, J., Zhong, Q. TM. iScience. 2022 Jan 22;25(2):103798. doi: 10.1016/j.isci.2022.103798. PMID: 35169688.
Pipeline for Generating High-Quality Spectral Libraries for DIA-MS Data. Manda, S. S., Noor, Z., Hains, P. G., Zhong, Q. TM. Current Protocols in Bioinformatics. 2021 Mar;1(3):e69. doi: 10.1002/cpz1.69. PMID: 33656278.
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE). Seneviratne, A. J., Peters, S., Clarke, D., Dausmann, M., Hecker, M., Tully, B., Hains, P. G., Zhong, Q. TM. Bioinformatics. 2021 Jul 29;37(24):4719-4726. doi: 10.1093/bioinformatics/btab563. PMID: 34323970.
On the feasibility of deep learning applications using raw mass spectrometry data. Joris Cadow, Matteo Manica, Roland Mathis, Roger R Reddel, Phillip J Robinson, Peter J Wild, Peter G Hains, Natasha Lucas, Qing Zhong, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez. Bioinformatics, Volume 37, Issue Supplement_1, July 2021, Pages i245–i253, doi.org/10.1093/bioinformatics/btab311
Role of POT1 in Human Cancer. Wu, Y., Poulos, R. C., Reddel, R. R. TM. Cancers. 2020 Sep 24;12(10):2739. doi: 10.3390/cancers12102739. PMID: 32987645.
Strategies to enable large-scale proteomics for reproducible research. Poulos, R. C., Hains, P. G., Shah, R., Lucas, N., Xavier, D. Manda, S. S., Anees, A., Koh, J., Mahboob, S., Wittman, M., Williams, S. G., Sykes, E., Hecker, M., Dausmann, M., Wouters, M. A., Ashman, K., Yang, J., Wild, P. J., deFazio, A., Balleine, R. L., Tully, B., Aebersold, R., Speed, T. P, Liu, Y., Reddel, R. R., Robinson, P. J., Zhong, Q. TM. Nature Communications. 2020 Jul 30;11(1):3793. doi: 10.1038/s41467-020-17641-3. PMID: 32732981.
Toffee - a highly efficient, lossless file format for DIA-MS. Tully, B. TM. Nature - Scientific Reports. 2020 Jun 2;10(1):8939. doi: 10.1038/s41598-020-65015-y. PMID: 32488104.
Addressing the challenges of high-throughput cancer tissue proteomics for clinical application. Tully, B., Balleine, R. L., Hains, P. G., Zhong, Q., Reddel, R. R., Robinson, P. J. TM. Proteomics. 2019 Nov;19(21-22):e1900109. doi: 10.1002/pmic.201900109. PMID: 31321850.
A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs. Peters, S., Hains, P. G., Lucas, N., Robinson, P. J., Tully, B. TM. ACS – Journal of Proteome Research. 2019 Mar 1;18(3):1019-1031. doi: 10.1021/acs.jproteome.8b00709. PMID: 30652484.
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE). Seneviratne, A. J., Peters, S., Clarke, D., Dausmann, M., Hecker, M., Tully, B., Hains, P. G., Zhong, Q. TM. Bioinformatics. 2021 Jul 29;37(24):4719-4726. doi: 10.1093/bioinformatics/btab563. PMID: 34323970.
Accelerated Barocycler Lysis and Extraction Sample Preparation for Clinical Proteomics by Mass Spectrometry. Lucas, N., Robinson, A. B., Epersen, M. M., Mahoob, S. Xavier, D., Xue, J., Balleine, R. L., deFazio, A., Hains, P. G., Robinson, P. J. TM. ACS – Journal of Proteome Research. 2019 Jan 4;18(1):399-405. doi: 10.1021/acs.jproteome.8b00684. PMID: 30444966.