Timothy J. Griffin

Department of Biochemistry, University of Minnesota

Research Area

Biography

Timothy J. Griffin has not added Biography.
If you are Timothy J. Griffin and would like to personalize this page please email our Author Liaison for assistance.

JoVE Journal Publications

ArticleTotal : 1	Year
Publication title	2025

Other Publications

Article	Year
Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in S... Analytical chemistry\| PubMed ID: 15889909	2005
A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry. Molecular & cellular proteomics : MCP\| PubMed ID: 16103422	2005
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. Journal of proteome research\| PubMed ID: 16602709	2006
Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes. Proteomics\| PubMed ID: 16888762	2006
Carbonylation of adipose proteins in obesity and insulin resistance: identification of adipocyte fatty acid-binding protein as a cellular target of 4-hydroxynonenal. Molecular & cellular proteomics : MCP\| PubMed ID: 17205980	2007
Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40. Nature cell biology\| PubMed ID: 17277771	2007
Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography-stable isotope labeling and tandem mass spectrometry. Proteomics\| PubMed ID: 17390297	2007
Preparative peptide isoelectric focusing as a tool for improving the identification of lysine-acetylated peptides from complex mixtures. Journal of proteome research\| PubMed ID: 17397211	2007
Proteomic mapping of 4-hydroxynonenal protein modification sites by solid-phase hydrazide chemistry and mass spectrometry. Analytical chemistry\| PubMed ID: 17437329	2007
PRR5, a novel component of mTOR complex 2, regulates platelet-derived growth factor receptor beta expression and signaling. The Journal of biological chemistry\| PubMed ID: 17599906	2007
Advancing mammalian cell culture engineering using genome-scale technologies. Trends in biotechnology\| PubMed ID: 17681628	2007
iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. Journal of proteome research\| PubMed ID: 17902639	2007
Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry. Molecular & cellular proteomics : MCP\| PubMed ID: 18045803	2008
Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis. PloS one\| PubMed ID: 18270585	2008
Oxidative stress and covalent modification of protein with bioactive aldehydes. The Journal of biological chemistry\| PubMed ID: 18445586	2008
Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PloS one\| PubMed ID: 18461186	2008
Quantitative proteomic profiling of muscle type-dependent and age-dependent protein carbonylation in rat skeletal muscle mitochondria. The journals of gerontology. Series A, Biological sciences and medical sciences\| PubMed ID: 19038828	2008
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva. Journal of proteome research\| PubMed ID: 19813771	2009
Systematic comparison of the human saliva and plasma proteomes. Proteomics. Clinical applications\| PubMed ID: 19898684	2009
Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response. Molecular & cellular proteomics : MCP\| PubMed ID: 19955088	2010
Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems. Journal of proteome research\| PubMed ID: 20184388	2010
Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry. Journal of the American Society for Mass Spectrometry\| PubMed ID: 20434358	2010
Global assessment of protein turnover in recombinant antibody producing myeloma cells. Journal of biotechnology\| PubMed ID: 20540971	2010
Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions. PloS one\| PubMed ID: 20567502	2010
LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics\| PubMed ID: 20821806	2010
Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential. Clinical proteomics\| PubMed ID: 20930922	2010
Mass spectrometric identification of phosphorylation sites in guanylyl cyclase A and B. Biochemistry\| PubMed ID: 20977274	2010
Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva. Journal of proteome research\| PubMed ID: 21142092	2011
Large-scale phosphoproteomics analysis of whole saliva reveals a distinct phosphorylation pattern. Journal of proteome research\| PubMed ID: 21299198	2011
Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery. Clinica chimica acta; international journal of clinical chemistry\| PubMed ID: 21889499	2011
Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery. Clinical proteomics\| PubMed ID: 21914210	2011
Three-dimensional peptide fractionation for highly sensitive nanoscale LC-based shotgun proteomic analysis of complex protein mixtures. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 21948405	2011
Deep metaproteomic analysis of human salivary supernatant. Proteomics\| PubMed ID: 22522805	2012
SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Molecular cell\| PubMed ID: 22575674	2012
A functional screen provides evidence for a conserved, regulatory, juxtamembrane phosphorylation site in guanylyl cyclase a and B. PloS one\| PubMed ID: 22590601	2012
Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm. Proteomics\| PubMed ID: 22623410	2012
Protein carbonylation and adipocyte mitochondrial function. The Journal of biological chemistry\| PubMed ID: 22822087	2012
Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures. Journal of proteome research\| PubMed ID: 22950739	2012
Fibroblast growth factor receptor 1 activation in mammary tumor cells promotes macrophage recruitment in a CX3CL1-dependent manner. PloS one\| PubMed ID: 23029290	2012
Mass spectrometry-based proteomics: basic principles and emerging technologies and directions. Advances in experimental medicine and biology\| PubMed ID: 23378000	2013
A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics\| PubMed ID: 23412978	2013
Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw. Oral diseases\| PubMed ID: 24286378	2015
Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN). Journal of proteome research\| PubMed ID: 24571364	2014
Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker. PloS one\| PubMed ID: 24748380	2014
A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics. Clinical proteomics\| PubMed ID: 25097468	2014
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. BMC genomics\| PubMed ID: 25149441	2014
Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. Journal of proteome research\| PubMed ID: 25301683	2014
Multi-omic data analysis using Galaxy. Nature biotechnology\| PubMed ID: 25658277	2015
Metaproteomic analysis using the Galaxy framework. Proteomics\| PubMed ID: 26058579	2015
mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation. Nature communications\| PubMed ID: 26074333	2015
Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics. Journal of proteome research\| PubMed ID: 26435507	2015
Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect monoclonal immunoglobulin light chains in serum and urine. Rapid communications in mass spectrometry : RCM\| PubMed ID: 26443406	2015
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. Microbiome\| PubMed ID: 26684897	2015
Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype. Journal of proteome research\| PubMed ID: 26903422	2016
AminoxyTMT: A novel multi-functional reagent for characterization of protein carbonylation. BioTechniques\| PubMed ID: 27071607	2016
Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression. Cell reports\| PubMed ID: 27134171	2016
RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification. Bioinformatics (Oxford, England)\| PubMed ID: 27153682	2016
Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease. International journal of chronic obstructive pulmonary disease\| PubMed ID: 27729784	2016
Plasma sphingolipids in HIV-associated chronic obstructive pulmonary disease. BMJ open respiratory research\| PubMed ID: 28409005	2017
An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Cancer research\| PubMed ID: 29092937	2017
Normalization of mass spectrometry data (NOMAD). Advances in biological regulation\| PubMed ID: 29174395	2018
ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction. Autophagy\| PubMed ID: 29313410	2018
Increased Indoleamine-2,3-Dioxygenase Activity Is Associated With Poor Clinical Outcome in Adults Hospitalized With Influenza in the INSIGHT FLU003Plus Study. Open forum infectious diseases\| PubMed ID: 29322062	2018
Salivary proteomics of healthy dogs: An in depth catalog. PloS one\| PubMed ID: 29329347	2018
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes\| PubMed ID: 29385081	2018
Multi-omic molecular profiling of lung cancer in COPD. The European respiratory journal\| PubMed ID: 29794131	2018
Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome. Scientific reports\| PubMed ID: 30022083	2018
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... Journal of proteome research\| PubMed ID: 30130115	2018
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 dev... Synapse (New York, N.Y.)\| PubMed ID: 30176067	2019
Plasma lipoproteome in Alzheimer's disease: a proof-of-concept study. Clinical proteomics\| PubMed ID: 30250409	2018
BAL Fluid Metaproteome in Acute Respiratory Failure. American journal of respiratory cell and molecular biology\| PubMed ID: 30382775	2018
Update on the moFF Algorithm for Label-Free Quantitative Proteomics. Journal of proteome research\| PubMed ID: 30511867	2019
Improve your Galaxy text life: The Query Tabular Tool. F1000Research\| PubMed ID: 30519459	2018
QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. Journal of proteome research\| PubMed ID: 30582332	2019
Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function. American journal of respiratory and critical care medicine\| PubMed ID: 30742544	2019
The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 30980333	2019
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. Molecular & cellular proteomics : MCP\| PubMed ID: 31235611	2019
The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends in cancer\| PubMed ID: 32101723	2020
Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. GigaScience\| PubMed ID: 32236523	2020
A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases. Journal of proteome research\| PubMed ID: 32396365	2020
Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform. Proteomes\| PubMed ID: 32650610	2020
Application of Proteomics in Sarcoidosis. American journal of respiratory cell and molecular biology\| PubMed ID: 32804537	2020
Survey of metaproteomics software tools for functional microbiome analysis. PloS one\| PubMed ID: 33170893	2020
Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms. Journal of proteome research\| PubMed ID: 33393790	2021
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. Clinical proteomics\| PubMed ID: 33413078	2021
Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of proteome research\| PubMed ID: 33683127	2021
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). medRxiv : the preprint server for health sciences\| PubMed ID: 33688669	2021
Metabolite profiles associated with disease progression in influenza infection. PloS one\| PubMed ID: 33798209	2021
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clinical proteomics\| PubMed ID: 33971807	2021
Novel 4-Hydroxybenzyl Adducts in Human Hemoglobin: Structures and Mechanisms of Formation. Chemical research in toxicology\| PubMed ID: 34110810	2021
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research\| PubMed ID: 34484688	2021
Perspectives on automated composition of workflows in the life sciences. F1000Research\| PubMed ID: 34804501	2021
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature communications\| PubMed ID: 34911965	2021
Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow. Proteomes\| PubMed ID: 35466239	2022
An overview of technologies for MS-based proteomics-centric multi-omics. Expert review of proteomics\| PubMed ID: 35466851	2022
Lung and Plasma Metabolome in HIV-Associated Obstructive Lung Disease. Journal of acquired immune deficiency syndromes (1999)\| PubMed ID: 35849661	2022
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations. Viruses\| PubMed ID: 36298760	2022
Galaxy Training: A powerful framework for teaching! PLoS computational biology\| PubMed ID: 36622853	2023
Lung proteome and metabolome endotype in HIV-associated obstructive lung disease. ERJ open research\| PubMed ID: 36949960	2023
An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples. Clinical proteomics\| PubMed ID: 37005570	2023
Integrative meta-omics in Galaxy and beyond. Environmental microbiome\| PubMed ID: 37420292	2023
Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients. Journal of proteome research\| PubMed ID: 37450889	2023
A Galaxy of informatics resources for MS-based proteomics. Expert review of proteomics\| PubMed ID: 37787106	2023
Discovery of Modified Metabolites, Secondary Metabolites, and Xenobiotics by Structure-Oriented LC-MS/MS. Chemical research in toxicology\| PubMed ID: 37862059	2023
Mass Spectrometry-Based Strategies for Assessing Human Exposure Using Hemoglobin Adductomics. Chemical research in toxicology\| PubMed ID: 37963067	2023
A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. mSphere\| PubMed ID: 38780289	2024
Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis. Research square\| PubMed ID: 38883770	2024
An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems\| PubMed ID: 38934598	2024
Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis. Respiratory research\| PubMed ID: 39256809	2024
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome. bioRxiv : the preprint server for biology\| PubMed ID: 39345414	2024
Dichotomous intronic polyadenylation profiles reveal multifaceted gene functions in the pan-cancer transcriptome. Experimental & molecular medicine\| PubMed ID: 39349823	2024
A constitutional isomer selective chemical proteomic strategy for system-wide profiling of protein lysine 5-hydroxylation. Chemical science\| PubMed ID: 39421203	2024
Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 39436599	2025
Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer. Scientific reports\| PubMed ID: 39755759	2025