Affiliation: Northeastern University
Surinova S, RadovÃ¡ L, Choi M, Srovnal J, Brenner H, Vitek O, et al
. Non-invasive prognostic protein biomarker signatures associated with colorectal cancer. EMBO Mol Med. 2015;7:1153-65 pubmed publisher
..These findings highlight the value of a simultaneous assessment of important prognostic disease characteristics within a single measurement. ..
Surinova S, Choi M, Tao S, SchÃ¼ffler P, Chang C, Clough T, et al
. Prediction of colorectal cancer diagnosis based on circulating plasma proteins. EMBO Mol Med. 2015;7:1166-78 pubmed publisher
..The data were deployed to develop and evaluate a five-protein biomarker signature for colorectal cancer detection. ..
Dogu E, Mohammad Taheri S, Abbatiello S, Bereman M, Maclean B, Schilling B, et al
. MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments. Mol Cell Proteomics. 2017;16:1335-1347 pubmed publisher
..They are available for use stand-alone, or for integration with automated pipelines. Although the examples focus on targeted proteomics, the statistical methods in this manuscript apply more generally to quantitative proteomics. ..
Galitzine C, Egertson J, Abbatiello S, Henderson C, PINO L, MacCoss M, et al
. Nonlinear Regression Improves Accuracy of Characterization of Multiplexed Mass Spectrometric Assays. Mol Cell Proteomics. 2018;17:913-924 pubmed publisher
..We implemented the nonlinear regression approach in the open-source R-based software MSstats, and advocate its general use for characterization of mass spectrometry-based assays. ..
Bemis K, Harry A, Eberlin L, Ferreira C, van de Ven S, Mallick P, et al
. Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments. Mol Cell Proteomics. 2016;15:1761-72 pubmed publisher
..This framework is available for use within the open-source R package Cardinal as part of a full pipeline for the processing, visualization, and statistical analysis of mass spectrometry imaging experiments. ..