Publications
View our complete publication list on Google Scholar or search PubMed.
Publication Metrics
- Total Citations: >50,185 (Google Scholar)
- h-index: >103
- Most Cited Paper: “Skyline: an open source document editor for creating and analyzing targeted proteomics experiments” (5,064+ citations)
Recent Publications
2025
Tissue-specific metabolomic signatures for a doublesex model of reduced sexual dimorphism
Coig R, Harrison B, Johnson R, MacCoss MJ, Promislow D
Royal Society Open Science 2025 Jul 9;12(7):250770
PubMed | DOI
Performance of novel tau antibodies across multiple modalities for Alzheimer’s disease assessment
Trivedi P, Forrest K, Fisher DW, Winstone JK, McMillan PJ, Valentine M, Postupna N, Wilson A, Bajwa T, MacCoss MJ, Keene CD, Darvas M, Kraemer BC, Hoofnagle AN, Latimer CS
Alzheimer’s & Dementia 2025 Jul;21(7):e70481
PubMed | DOI
A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data
Sanders J, Wen B, Rudnick PA, Johnson RS, Wu CC, Riffle M, Oh S, MacCoss MJ, Noble WS
Nature Methods 2025 Jul;22(7):1447-1453
PubMed | DOI
Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome
Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ
Nature Communications 2025 Jul 1;16(1):5447
PubMed | DOI
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment
Wen B, Freestone J, Riffle M, MacCoss MJ, Noble WS, Keich U
Nature Methods 2025 Jul;22(7):1454-1463
PubMed | DOI
Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics - Beyond identification lists
Hsu C, Shulman N, Stewart H, Petzoldt J, Pashkova A, Plubell DL, Denisov E, Hagedorn B, Damoc E, MacLean BX, Remes P, Canterbury JD, Makarov A, Hock C, Zabrouskov V, Wu CC, MacCoss MJ
bioRxiv 2025 Jun 25 (Preprint)
PubMed | DOI
Improved quantitative accuracy in data-independent acquisition proteomics via retention time boundary imputation
Harris L, Riffle M, Noble WS, MacCoss MJ
bioRxiv 2025 May 31 (Preprint)
PubMed | DOI
Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer
Plubell DL, Huang E, Spencer SE, Poston KL, Montine TJ, MacCoss MJ
Journal of Proteome Research 2025 Jun 6;24(6):2885-2891
PubMed | DOI
Molecular basis of SIFI activity in the integrated stress response
Yang Z, Haakonsen DL, Heider M, Witus SR, Zelter A, Beschauner T, MacCoss MJ, Rapé M
Nature 2025 Jul;643(8073):1117-1126
PubMed | DOI
Quantification of glucagon and oxyntomodulin by protein precipitation-immunoaffinity enrichment-LC-MS/MS
Becker JO, Shijo SK, Huynh HH, Forrest KL, MacCoss MJ, Emrick MA, Goonatilleke E, Hoofnagle AN
Journal of Mass Spectrometry and Advances in the Clinical Lab 2025 Apr;36:37-45
PubMed | DOI
The Need for Better Validation: Evaluating Aptamer and Proximity Extension Assays for Large-Scale Clinical Proteomics Studies
Hoofnagle AN, MacCoss MJ
Clinical Chemistry 2025 Apr 24
PubMed | DOI
Open-Source and FAIR Research Software for Proteomics
Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE
Journal of Proteome Research 2025 May 2;24(5):2222-2234
PubMed | DOI
Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data
Vidović D, Shamsaei B, Schürer SC, Kogan P, Chojnacki S, Kouril M, Medvedovic M, Niu W, Azeloglu EU, Birtwistle MR, Chen Y, Chen T, Hansen J, Hu B, Iyengar R, Jayaraman G, Li H, Liu T, Sobie EA, Xiong Y, Berberich MJ, Bradshaw G, Chung M, Everley RA, Gaudio B, Hafner M, Kalocsay M, Mills CE, Nariya MK, Sorger PK, Subramanian K, Victor C, Banuelos M, Dardov V, Holewinski R, Manalo DM, Mandefro B, Matlock AD, Ornelas L, Sareen D, Svendsen CN, Vaibhav V, Van Eyk JE, Venkatraman V, Finkbiener S, Fraenkel E, Rothstein J, Thompson L, Asiedu J, Carr SA, Christianson KE, Davison D, Dele-Oni DO, DeRuff KC, Egri SB, Jacome ASV, Jaffe JD, Lam D, Litichevskiy L, Lu X, Mullahoo J, Officer A, Papanastasiou M, Peckner R, Toder C, Blanchard J, Bula M, Ko T, Tsai LH, Young JZ, Sharma V, Pillai A, Meller J, MacCoss MJ
Molecular & Cellular Proteomics 2025 Mar 13;24(7):100947
PubMed | DOI
Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding
Feldman D, Sims JN, Li X, Johnson R, Gerben S, Kim DE, Richardson C, Koepnick B, Eisenach H, Hicks DR, Yang EC, Wicky BIM, Milles LF, Bera AK, Kang A, Brackenbrough E, Joyce E, Sankaran B, Lubner JM, Goreshnik I, Vafeados D, Allen A, Stewart L, MacCoss MJ, Baker D
bioRxiv 2025 Feb 28 (Preprint)
PubMed | DOI
Biomarkers, Proteoforms, and Mass Spectrometry-Based Assays for Diabetes Clinical Research
Nierves LA, Lin TT, Moradian A, Shen Q, Sechi S, MacCoss MJ, Qu J, van Eyk JE, Hoofnagle AN, Qian WJ
Journal of Clinical Endocrinology & Metabolism 2025 May 19;110(6):1514-1523
PubMed | DOI
Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines
Riffle M, Zelter A, Jaschob D, Hoopmann MR, Faivre DA, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N
Journal of Proteome Research 2025 Apr 4;24(4):1895-1906
PubMed | DOI
Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes
Bramer LM, Nakayasu ES, Flores JE, Van Eyk JE, MacCoss MJ, Parikh HM, Metz TO, Webb-Robertson BM
Scientific Data 2025 Jan 20;12(1):112
PubMed | DOI
2024
Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics
Remes PM, Jacob CC, Heil LR, Shulman N, MacLean BX, MacCoss MJ
Journal of Proteome Research 2024 Dec 6;23(12):5476-5486
PubMed | DOI
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
Wen B, Hsu C, Zeng WF, Riffle M, Chang A, Mudge M, Nunn B, Berg MD, Villén J, MacCoss MJ, Noble WS
bioRxiv 2024 Oct 18 (Preprint)
PubMed | DOI
Detection and Quantification of Drug-Protein Adducts in Human Liver
Zelter A, Riffle M, Shteynberg DD, Zhong G, Riddle EB, Hoopmann MR, Jaschob D, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N
Journal of Proteome Research 2024 Nov 1;23(11):5143-5152
PubMed | DOI
2023
Sampling the proteome by emerging single-molecule and mass spectrometry methods
MacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu M, Slavov N
Nature Methods 2023 Mar;20(3):339-346
PubMed | DOI
A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer’s disease
Merrihew GE, Park J, Plubell D, Searle BC, Keene CD, Larson EB, Bateman R, Perrin RJ, Chhatwal JP, Farlow MR, McLean CA, Ghetti B, Newell KL, Frosch MP, Montine TJ, MacCoss MJ
Scientific Data 2023 Apr 14;10(1):206
PubMed | DOI
Research Themes
Our publications span several key areas:
Method Development
- Targeted proteomics workflows
- Data-independent acquisition (DIA)
- Quality control and standardization
- Cross-platform harmonization
Software Development
- Open-source proteomics tools
- Data analysis platforms
- Spectral libraries and databases
- Workflow automation
Clinical Applications
- Biomarker discovery and validation
- Alzheimer’s disease research
- Precision medicine applications
- Large-scale clinical studies
Computational Proteomics
- Database search algorithms
- Statistical frameworks
- Machine learning applications
- Data processing pipelines
Data Availability
Most recent publications include:
- Skyline documents available on Panorama Public
- Raw mass spectrometry data deposited in public repositories
- Analysis code available on GitHub: github.com/uw-maccosslab
This list represents selected publications. For a complete and up-to-date list, please visit our Google Scholar profile or PubMed search.