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List of works by Michael J MacCoss

A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack

scientific article published on 10 April 2018

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

scientific article published on 11 April 2018

A Stem-Loop Structure in Potato Leafroll Virus Open Reading Frame 5 (ORF5) Is Essential for Readthrough Translation of the Coat Protein ORF Stop Codon 700 Bases Upstream.

scientific article

A correlation algorithm for the automated quantitative analysis of shotgun proteomics data

scientific article

A cross-platform toolkit for mass spectrometry and proteomics

scientific article

A deeper look into Comet--implementation and features

scientific article published on 27 June 2015

A framework for installable external tools in Skyline

scientific article

A glutamate-alanine-leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defence and killing of macrophages: role of cyclic diGMP.

scientific article published in June 2005

A high voltage asymmetric waveform generator for FAIMS.

scientific article

A major deletion in the surfactant protein-B gene causing lethal respiratory distress.

scientific article published in April 2007

A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain

scientific article published on 17 July 2017

A method for the comprehensive proteomic analysis of membrane proteins ⬇️

scientific article published on April 14, 2003

A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome.

scientific article published on 14 April 2012

A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva.

scientific article

ABRF-PRG07: advanced quantitative proteomics study

scientific article

Accounting for population variation in targeted proteomics

scientific article published on 16 December 2013

Age modifies respiratory complex I and protein homeostasis in a muscle type-specific manner

scientific article

Aminoglycoside antibiotics induce bacterial biofilm formation

scientific journal article

An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments

scientific article

An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domain

scientific article

An expansive human regulatory lexicon encoded in transcription factor footprints

scientific article

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries

scientific article

Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics

scientific article

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

scientific article published on 08 December 2007

Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography

scientific article published on 30 January 2017

Bindin from a sea star

scientific article (publication date: 2009)

Biomarkers of organophosphorus (OP) exposures in humans ⬇️

scientific article published on July 8, 2011

Bruton's tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling

scientific article published on 26 May 2009

Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories

article by Lindsay K. Pino et al published 11 October 2018 in Analytical Chemistry

Code developments to improve the efficiency of automated MS/MS spectra interpretation

scientific article published in May 2002

Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut.

scientific article

Comparative analysis of the transcriptome across distant species

scientific article

Comparison between procedures using SDS for shotgun proteomic analyses of complex samples ⬇️

scientific article published on June 8, 2011

Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics

scientific article

Comparison of database search strategies for high precursor mass accuracy MS/MS data

scientific article

Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries

Computational analysis of quantitative proteomics data using stable isotope labeling

scientific article

Computational analysis of shotgun proteomics data

scientific article

Computational and Statistical Analysis of Protein Mass Spectrometry Data ⬇️

scientific article published on January 26, 2012

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

scientific article

Crux: rapid open source protein tandem mass spectrometry analysis

scientific article published on 9 September 2014

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics

scientific article

Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry

scientific article

Development of Selected Reaction Monitoring Methods to Systematically Quantify Kinase Abundance and Phosphorylation Stoichiometry in Human Samples

scientific article published in January 2017

Direct Maximization of Protein Identifications from Tandem Mass Spectra ⬇️

scientific article published on November 3, 2011

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

scientific article published on October 30, 2012

Distinct roles of FKF1, Gigantea, and Zeitlupe proteins in the regulation of Constans stability in Arabidopsis photoperiodic flowering

scientific article

Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures

scientific article

Duplication and Selection on Abalone Sperm Lysin in an Allopatric Population

scientific article published on 13 July 2007

Effects of Column and Gradient Lengths on Peak Capacity and Peptide Identification in Nanoflow LC-MS/MS of Complex Proteomic Samples ⬇️

scientific article published on November 30, 2012

Effects of modified digestion schemes on the identification of proteins from complex mixtures

scientific article published on March 2006

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data

scientific article

Estimating relative abundances of proteins from shotgun proteomics data ⬇️

scientific article published on November 19, 2012

Evaluation of Front-End Higher Energy Collision-Induced Dissociation on a Benchtop Dual-Pressure Linear Ion Trap Mass Spectrometer for Shotgun Proteomics ⬇️

scientific article published on January 12, 2012

Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry

scientific article published on 24 July 2017

Evidence for a post-translational modification, aspartyl aldehyde, in a photosynthetic membrane protein

scientific article published in July 2004

Evidence for lysine acetylation in the coat protein of a polerovirus

scientific article published on 17 June 2014

Evidence of the biochemical basis of host virulence in the greenbug aphid, Schizaphis graminum (Homoptera: Aphididae).

scientific article published on 18 March 2014

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

scientific article

Functional diversification and evolution of antifreeze proteins in the antarctic fish Lycodichthys dearborni

scientific article

Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.

scientific article published on 8 July 2013

Garrod's fourth inborn error of metabolism solved by the identification of mutations causing pentosuria

scientific article published on 31 October 2011

Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus

scientific article

Global proteomics and pathway analysis of pressure-overload-induced heart failure and its attenuation by mitochondrial-targeted peptides

scientific article published on 09 August 2013

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry

scientific article

High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection

scientific article published on 7 July 2010

Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments

scientific article published on 27 February 2018

Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase

scientific article

Hyaluronan enhances wound repair and increases collagen III in aged dermal wounds

scientific article

Identification and characterization of biomarkers of organophosphorus exposures in humans

scientific article

Identification of Peptide Features in Precursor Spectra Using Hardklör and Krönik ⬇️

scientific article published on March 1, 2012

Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex

scientific article published on 31 January 2018

Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling ⬇️

scientific article published on June 10, 2011

Implementation of statistical process control for proteomic experiments via LC MS/MS

scientific article

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows

scientific article published in 2019

Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions

scientific article published on 11 July 2007

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis

article by Robert J Chalkley et al published January 2019 in Molecular & Cellular Proteomics

Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry

scientific article published on April 2015

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking

scientific article published on July 2010

Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex

scientific article

Kojak: efficient analysis of chemically cross-linked protein complexes.

scientific article

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data

scientific article

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

scientific article

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments

scientific article

MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.

scientific article published on January 2004

Mass spectrometry and next-generation sequencing reveal an abundant and rapidly evolving abalone sperm protein

scientific article

Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA).

scientific article

Measurement of human surfactant protein-B turnover in vivo from tracheal aspirates using targeted proteomics

scientific article

Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides

scientific article published on 01 December 2005

Metabolic Interplay between the Asian Citrus Psyllid and Its Profftella Symbiont: An Achilles' Heel of the Citrus Greening Insect Vector

scientific article published on 18 November 2015

Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis

scientific article published in September 2004

Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics

scientific journal article

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

scientific article published on October 19, 2011

Model System-Guided Protein Interaction Mapping for Virus Isolated from Phloem Tissue

scientific article

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

scientific article

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

scientific article

Molecular mechanisms underlying genotype-dependent responses to dietary restriction.

scientific article published on 11 August 2013

Multiplexed MS/MS for improved data-independent acquisition

scientific article

Multiplexed peptide analysis using data-independent acquisition and Skyline

scientific article

Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows

scientific article

New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins

scientific article

New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening

scientific article

Nitric-oxide Synthase Forms N-NO-pterin and S-NO-Cys: IMPLICATIONS FOR ACTIVITY, ALLOSTERY, AND REGULATION

scientific article

Nonlinear regression improves accuracy of characterization of multiplexed mass spectrometric assays

scientific article published on 9 February 2018

Organellar proteomics reveals Golgi arginine dimethylation

scientific article

Overexpression of catalase targeted to mitochondria attenuates murine cardiac aging.

scientific article

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline

scholarly article by Vagisha Sharma published in June 2018

Panorama: a targeted proteomics knowledge base

scientific article

Peptide charge state determination for low-resolution tandem mass spectra.

scientific article published in January 2005

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

scientific article published on 27 July 2015

Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures

scientific article

Posterior error probabilities and false discovery rates: two sides of the same coin

scientific article published on 04 December 2007

Posttranslational modifications in the CP43 subunit of photosystem II

scientific article

Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection

scientific article published on 29 April 2015

Precursor charge state prediction for electron transfer dissociation tandem mass spectra

scientific article published on October 2010

Probability-based validation of protein identifications using a modified SEQUEST algorithm

scientific article published in November 2002

Proteogenomic database construction driven from large scale RNA-seq data

scientific article

Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures ⬇️

scientific article published on November 2, 2012

Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila

scientific article published on May 2009

Proteomic solutions for analytical challenges associated with alcohol research

scientific article published on January 2008

Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus).

scientific article published on 06 May 2009

Quantification by nano liquid chromatography parallel reaction monitoring mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots

scientific article published on 23 January 2017

Quantitative MS for proteomics: teaching a new dog old tricks

scientific article published on 01 August 2005

Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap

scientific article

Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems.

scientific article

Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway

scientific article published on 20 July 2007

Quantitative proteomic analysis of mammalian organisms using metabolically labeled tissues

scientific article published on 01 January 2007

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

scientific article published on 11 February 2016

Rapid and accurate peptide identification from tandem mass spectra

scientific article published on 28 May 2008

Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring mass spectrometry

scientific article published on 10 June 2013

Rapid empirical discovery of optimal peptides for targeted proteomics

scientific article published on 6 November 2011

Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs

scholarly article

Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex

scientific article

Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards

scientific article published on January 2016

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

scientific article

Shotgun identification of protein modifications from protein complexes and lens tissue

scientific article

Shotgun proteomics: tools for the analysis of complex biological systems

scientific article (publication date: June 2002)

Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility

scientific article published in May 2003

Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin

scientific article published on 4 December 2017

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

scientific article published on 9 February 2010

Stable Isotope Labeling Reveals Novel Insights Into Ubiquitin-Mediated Protein Aggregation With Age, Calorie Restriction, and Rapamycin Treatment

scientific article published in April 2018

Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa

scientific article published on 24 May 2016

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

scientific article

Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure

scientific article published on 8 March 2016

Subacute calorie restriction and rapamycin discordantly alter mouse liver proteome homeostasis and reverse aging effects

scientific article

The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses

article

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

scientific article

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

scientific article published on 18 March 2013

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

scientific article published on 09 July 2017

The development of selected reaction monitoring methods for targeted proteomics via empirical refinement.

scientific article published on April 2012

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

scientific article

Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA in Arabidopsis thaliana

Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis

scientific article published in 2019

Topograph, a software platform for precursor enrichment corrected global protein turnover measurements

scientific article

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

scientific article published on 24 July 2008

Using BiblioSpec for creating and searching tandem MS peptide libraries

scientific article

Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments

scientific article

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

article

Using iRT, a normalized retention time for more targeted measurement of peptides ⬇️

scientific article published on April 1, 2012

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

scientific article published on January 2016

Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development

scientific article

ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins

scientific article

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