MacCoss, Michael J.

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., & MacCoss, M. J. (2010) · Bioinformatics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 4,697

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 2,424

How many human proteoforms are there?

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., et al. (2018) · Nature Chemical Biology

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 907

Molecular architecture and assembly of the DDB1–CUL4A ubiquitin ligase machinery

Angers, S., Li, T., Yi, X., MacCoss, M. J., Moon, R. T., & Zheng, N. (2006) · Nature

Ubiquitin and proteasome pathwaysEnzyme Structure and Function

Cited by 674

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

Käll, L., Storey, J. D., MacCoss, M. J., & Noble, W. S. (2008) · Journal of Proteome Research

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 607

The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo

Vincow, E. S., Merrihew, G., Thomas, R. E., Shulman, N. J., Beyer, R. P., MacCoss, M. J., & Pallanck, L. J. (2013) · Proceedings of the National Academy of Sciences

Autophagy in Disease and TherapyParkinson's Disease Mechanisms and Treatments

Cited by 478

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

The, M., MacCoss, M. J., Noble, W. S., & Käll, L. (2016) · Journal of the American Society for Mass Spectrometry

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 454

Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis

Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., & Yates, J. R. (2004) · Analytical Chemistry

Advanced Proteomics Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

Cited by 386

The KLHL12–Cullin-3 ubiquitin ligase negatively regulates the Wnt–β-catenin pathway by targeting Dishevelled for degradation

Angers, S., Thorpe, C. J., Biechele, T. L., Goldenberg, S. J., Zheng, N., MacCoss, M. J., & Moon, R. T. (2006) · Nature Cell Biology

Wnt/β-catenin signaling in development and cancerUbiquitin and proteasome pathways

Cited by 364

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma

Abbatiello, S. E., Schilling, B., Mani, D. R., Zimmerman, L. J., Hall, S. C., MacLean, B., Albertolle, M., Allen, S., Burgess, M., Cusack, M. P., et al. (2015) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 215

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A. I., Pedrioli, P. G. A., et al. (2017) · Nature Methods

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 203

Mitochondrial proteome remodelling in pressure overload-induced heart failure: the role of mitochondrial oxidative stress

Dai, D.-F., Hsieh, E. J., Liu, Y., Chen, T., Beyer, R. P., Chin, M. T., MacCoss, M. J., & Rabinovitch, P. S. (2012) · Cardiovascular Research

Mitochondrial Function and PathologyCardiac Ischemia and Reperfusion

Cited by 178

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

Ting, Y. S., Egertson, J. D., Payne, S. H., Kim, S., MacLean, B., Käll, L., Aebersold, R., Smith, R. D., Noble, W. S., & MacCoss, M. J. (2015) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 175

Molecular mechanisms underlying genotype‐dependent responses to dietary restriction

Schleit, J., Johnson, S. C., Bennett, C. F., Simko, M., Trongtham, N., Castanza, A., Hsieh, E. J., Moller, R. M., Wasko, B. M., Delaney, J. R., et al. (2013) · Aging Cell

Genetics, Aging, and Longevity in Model OrganismsAutophagy in Disease and Therapy

Cited by 159

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

Prakash, A., Tomazela, D. M., Frewen, B., MacLean, B., Merrihew, G., Peterman, S., & MacCoss, M. J. (2009) · Journal of Proteome Research

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 147

Rapamycin transiently induces mitochondrial remodeling to reprogram energy metabolism in old hearts

Chiao, Y. A., Kolwicz, S. C., Basisty, N., Gagnidze, A., Zhang, J., Gu, H., Djukovic, D., Beyer, R. P., Raftery, D., MacCoss, M., et al. (2016) · Aging

Autophagy in Disease and TherapyMitochondrial Function and Pathology

Cited by 128

Rapid empirical discovery of optimal peptides for targeted proteomics

Stergachis, A. B., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., & MacCoss, M. J. (2011) · Nature Methods

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 110

Putting humpty dumpty back together again: what does protein quantification mean in bottom-up proteomics?

Plubell, D. L., Käll, L., Webb-Robertson, B.-J., Bramer, L. M., Ives, A., Kelleher, N. L., Smith, L. M., Montine, T. J., Wu, C. C., & MacCoss, M. J. (2022) · Journal of Proteome Research

Advanced Proteomics Techniques and ApplicationsAdvanced Biosensing Techniques and Applications

Cited by 85

Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective

Vincow, E. S., Thomas, R. E., Merrihew, G. E., Shulman, N. J., Bammler, T. K., MacDonald, J. W., MacCoss, M. J., & Pallanck, L. J. (2019) · Autophagy

Autophagy in Disease and TherapyUbiquitin and proteasome pathways

Cited by 54

Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection

Wojcik, R., Li, Y., MacCoss, M. J., & Dovichi, N. J. (2012) · Talanta

Mass Spectrometry Techniques and ApplicationsAdvanced Proteomics Techniques and Applications

Cited by 43

Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer’s disease

Huang, Z., Merrihew, G. E., Larson, E. B., Park, J., Plubell, D., Fox, E. J., Montine, K. S., Latimer, C. S., Dirk Keene, C., Zou, J. Y., et al. (2023) · Nature Communications

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 37

Discovery and Targeted LC-MS/MS of Purified Polerovirus Reveals Differences in the Virus-Host Interactome Associated with Altered Aphid Transmission

Cilia, M., Peter, K. A., Bereman, M. S., Howe, K., Fish, T., Smith, D., Gildow, F., MacCoss, M. J., Thannhauser, T. W., & Gray, S. M. (2012) · PLoS ONE

Plant Virus Research StudiesPhytoplasmas and Hemiptera pathogens

Cited by 35

De novo design of high-affinity protein binders to bioactive helical peptides

Vázquez Torres, S., Leung, P. J. Y., Lutz, I. D., Venkatesh, P., Watson, J. L., Hink, F., Huynh, H.-H., Yeh, A. H.-W., Juergens, D., Bennett, N. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 22

Hematopoietic Protein-1 Regulates the Actin Membrane Skeleton and Membrane Stability in Murine Erythrocytes

Chan, M. M., Wooden, J. M., Tsang, M., Gilligan, D. M., Hirenallur-S, D. K., Finney, G. L., Rynes, E., MacCoss, M., Ramirez, J. A., Park, H., et al. (2013) · PLoS ONE

Erythrocyte Function and PathophysiologyHemoglobinopathies and Related Disorders

Cited by 20