Michael J. MacCoss
YOU?
Author Swipe
View article: MTOR AS AN IMMUNE MEDIATOR OF THE FLASH EFFECT
MTOR AS AN IMMUNE MEDIATOR OF THE FLASH EFFECT Open
View article: Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics Open
View article: The ProteomeXchange consortium in 2026: making proteomics data FAIR
The ProteomeXchange consortium in 2026: making proteomics data FAIR Open
The ProteomeXchange consortium of proteomics resources (http://www.proteomexchange.org) was established to standardize open data practices in the mass spectrometry (MS)-based proteomics field. Here, we describe the main developments in Pro…
View article: Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists
Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists Open
Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbitrap Astral Zoom mass spectrometer (MS) …
View article: The companion dog as a translational model for Alzheimer's disease: Development of a longitudinal research platform and <i>post mortem</i> protocols
The companion dog as a translational model for Alzheimer's disease: Development of a longitudinal research platform and <i>post mortem</i> protocols Open
INTRODUCTION Canine cognitive dysfunction is a valuable model for Alzheimer's disease (AD) and Alzheimer's disease related dementias (ADRD) due to condensed lifespan, naturally occurring clinical signs, genetic diversity, shared environmen…
View article: Improvements to Casanovo, a deep learning <i>de novo</i> peptide sequencer
Improvements to Casanovo, a deep learning <i>de novo</i> peptide sequencer Open
Casanovo is a state-of-the-art deep learning model for de novo peptide sequencing from mass spectrometry proteomics data. Here we report on a series of enhancements to Casanovo, aimed at improving the interpretability of the scores assigne…
View article: Tissue-specific metabolomic signatures for a <i>doublesex</i> model of reduced sexual dimorphism
Tissue-specific metabolomic signatures for a <i>doublesex</i> model of reduced sexual dimorphism Open
Sex has a major effect on the metabolome. However, we do not yet understand the degree to which differences in metabolism are associated with anatomical dimorphism and modulated by sex-specific tissues. In the fruit fly, Drosophila melanog…
View article: Corrigendum to "Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data".
Corrigendum to "Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data". Open
View article: Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome
Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome Open
View article: Performance of novel tau antibodies across multiple modalities for Alzheimer's disease assessment
Performance of novel tau antibodies across multiple modalities for Alzheimer's disease assessment Open
INTRODUCTION Epitope‐specific antibodies are crucial for accurately identifying pathologic forms of proteins like hyperphosphorylated tau in Alzheimer's disease (AD). METHODS We developed monoclonal antibodies targeting phosphorylated tau …
View article: Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment Open
View article: Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics – Beyond identification lists
Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics – Beyond identification lists Open
Mass spectrometry instrumentation continues to evolve rapidly yet quantifying these advances beyond conventional peptide and protein detections remain challenging. Here, we evaluate a modified Orbitrap Astral Zoom mass spectrometer (MS) pr…
View article: Improved quantitative accuracy in data-independent acquisition proteomics via retention time boundary imputation
Improved quantitative accuracy in data-independent acquisition proteomics via retention time boundary imputation Open
The traditional approaches to handling missing values in DIA proteomics are to either remove high-missingness proteins or impute them with statistical procedures. Both have their disadvantages—removal can limit statistical power, while imp…
View article: Molecular basis of SIFI activity in the integrated stress response
Molecular basis of SIFI activity in the integrated stress response Open
Chronic stress response activation impairs cell survival and causes devastating degenerative diseases 1–3 . Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor of the integrated stress response …
View article: Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer
Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer Open
Mass spectrometry based targeted proteomics methods provide a sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a pro…
View article: Open-Source and FAIR Research Software for Proteomics
Open-Source and FAIR Research Software for Proteomics Open
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of…
View article: Quantification of glucagon and oxyntomodulin by protein precipitation-immunoaffinity enrichment-LC-MS/MS
Quantification of glucagon and oxyntomodulin by protein precipitation-immunoaffinity enrichment-LC-MS/MS Open
We have validated a method with a highly detailed standard operating procedure. We have characterized calibration materials to help maintain accuracy and achieve between-day and between-laboratory harmonization. The assay will be beneficia…
View article: Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data
Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data Open
View article: Biomarkers, Proteoforms, and Mass Spectrometry–Based Assays for Diabetes Clinical Research
Biomarkers, Proteoforms, and Mass Spectrometry–Based Assays for Diabetes Clinical Research Open
The prevalence of diabetes, particularly type 2 diabetes, has reached epidemic proportions globally. The number of patients with type 1 diabetes (T1D) is also increasing rapidly. Despite advancements in understanding the pathogenesis of di…
View article: Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines
Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines Open
Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein-protein interaction studies, biomarker discovery, and …
View article: Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding
Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding Open
Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecul…
View article: Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes
Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes Open
View article: Open-source and FAIR Research Software for Proteomics
Open-source and FAIR Research Software for Proteomics Open
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of…
View article: The molecular basis of integrated stress response silencing
The molecular basis of integrated stress response silencing Open
Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. To counteract this, cells deploy dedicated silencing factors, such as the E3 ligase SIFI that terminates the mitochondrial stress respon…
View article: Limelight - An open, web-based tool for visualizing, sharing, and analyzing mass spectrometry data from DDA pipelines
Limelight - An open, web-based tool for visualizing, sharing, and analyzing mass spectrometry data from DDA pipelines Open
Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein-protein interaction studies, biomarker discovery, and …
View article: 387 Identification of novel T cell receptor (TCR) target to brachyury for the development of T cell-based immunotherapy of chordoma and other solid tumors
387 Identification of novel T cell receptor (TCR) target to brachyury for the development of T cell-based immunotherapy of chordoma and other solid tumors Open
View article: Data-independent acquisition proteomic analysis of the brain microvasculature in Alzheimer’s disease identifies major pathways of dysfunction and upregulation of cytoprotective responses
Data-independent acquisition proteomic analysis of the brain microvasculature in Alzheimer’s disease identifies major pathways of dysfunction and upregulation of cytoprotective responses Open
Brain microvascular dysfunction is an important feature of Alzheimer’s disease (AD). To better understand the brain microvascular molecular signatures of AD, we processed and analyzed isolated human brain microvessels by data-independent a…
View article: Carafe enables high quality <i>in silico</i> spectral library generation for data-independent acquisition proteomics
Carafe enables high quality <i>in silico</i> spectral library generation for data-independent acquisition proteomics Open
Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of …
View article: Figure 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Figure 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
PDC study summary page offering a comprehensive overview of both data and metadata.
View article: Table 1 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Table 1 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Available data types in the proteomic data commons