Timothy J. Griffin

Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae.

A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry.

Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics.

Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes.

Carbonylation of adipose proteins in obesity and insulin resistance: identification of adipocyte fatty acid-binding protein as a cellular target of 4-hydroxynonenal.

Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40.

Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography-stable isotope labeling and tandem mass spectrometry.

Preparative peptide isoelectric focusing as a tool for improving the identification of lysine-acetylated peptides from complex mixtures.

Proteomic mapping of 4-hydroxynonenal protein modification sites by solid-phase hydrazide chemistry and mass spectrometry.

PRR5, a novel component of mTOR complex 2, regulates platelet-derived growth factor receptor beta expression and signaling.

Advancing mammalian cell culture engineering using genome-scale technologies.

iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer.

Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry.

Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis.

Oxidative stress and covalent modification of protein with bioactive aldehydes.

Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor.

Quantitative proteomic profiling of muscle type-dependent and age-dependent protein carbonylation in rat skeletal muscle mitochondria.

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

Systematic comparison of the human saliva and plasma proteomes.

Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response.

Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems.

Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry.

Global assessment of protein turnover in recombinant antibody producing myeloma cells.

Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions.

LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments.

Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential.

Mass spectrometric identification of phosphorylation sites in guanylyl cyclase A and B.

Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva.

Large-scale phosphoproteomics analysis of whole saliva reveals a distinct phosphorylation pattern.

Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery.

Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery.

Three-dimensional peptide fractionation for highly sensitive nanoscale LC-based shotgun proteomic analysis of complex protein mixtures.

Deep metaproteomic analysis of human salivary supernatant.

SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling.

A functional screen provides evidence for a conserved, regulatory, juxtamembrane phosphorylation site in guanylyl cyclase a and B.

Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.

Protein carbonylation and adipocyte mitochondrial function.

Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures.

Fibroblast growth factor receptor 1 activation in mammary tumor cells promotes macrophage recruitment in a CX3CL1-dependent manner.

Mass spectrometry-based proteomics: basic principles and emerging technologies and directions.

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw.

Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN).

Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker.

A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

Multi-omic data analysis using Galaxy.

Metaproteomic analysis using the Galaxy framework.

mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation.

Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.

Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect monoclonal immunoglobulin light chains in serum and urine.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype.

AminoxyTMT: A novel multi-functional reagent for characterization of protein carbonylation.

Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression.

RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification.

Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease.

Plasma sphingolipids in HIV-associated chronic obstructive pulmonary disease.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

Normalization of mass spectrometry data (NOMAD).

ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction.

Increased Indoleamine-2,3-Dioxygenase Activity Is Associated With Poor Clinical Outcome in Adults Hospitalized With Influenza in the INSIGHT FLU003Plus Study.

Salivary proteomics of healthy dogs: An in depth catalog.

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

Multi-omic molecular profiling of lung cancer in COPD.

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome.

Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.

Quantitative proteomics of forebrain subcellular fractions in fragile X mental retardation 1 knockout mice following acute treatment with 2-Methyl-6-(phenylethynyl)pyridine: Relevance to developmental study of schizophrenia.

Plasma lipoproteome in Alzheimer's disease: a proof-of-concept study.

BAL Fluid Metaproteome in Acute Respiratory Failure.

Update on the moFF Algorithm for Label-Free Quantitative Proteomics.

Improve your Galaxy text life: The Query Tabular Tool.

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics.

Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function.

The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.

metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.

A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases.

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.

Application of Proteomics in Sarcoidosis.

Survey of metaproteomics software tools for functional microbiome analysis.

Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.

Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics.

Updates on metaQuantome Software for Quantitative Metaproteomics.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

Metabolite profiles associated with disease progression in influenza infection.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

Novel 4-Hydroxybenzyl Adducts in Human Hemoglobin: Structures and Mechanisms of Formation.

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.

Perspectives on automated composition of workflows in the life sciences.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.

Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow.

An overview of technologies for MS-based proteomics-centric multi-omics.

Lung and Plasma Metabolome in HIV-Associated Obstructive Lung Disease.

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.

Galaxy Training: A powerful framework for teaching!

Lung proteome and metabolome endotype in HIV-associated obstructive lung disease.

An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.

Integrative meta-omics in Galaxy and beyond.

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.

A Galaxy of informatics resources for MS-based proteomics.

Discovery of Modified Metabolites, Secondary Metabolites, and Xenobiotics by Structure-Oriented LC-MS/MS.

Mass Spectrometry-Based Strategies for Assessing Human Exposure Using Hemoglobin Adductomics.

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.

Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.

An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease.

Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.

Dichotomous intronic polyadenylation profiles reveal multifaceted gene functions in the pan-cancer transcriptome.

A constitutional isomer selective chemical proteomic strategy for system-wide profiling of protein lysine 5-hydroxylation.

Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.

Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.