Author
Amy-Joan L. Ham
Other affiliations: Veterans Health Administration, Belmont University, Vanderbilt University Medical Center ...read more
Bio: Amy-Joan L. Ham is an academic researcher from Vanderbilt University. The author has contributed to research in topics: Phosphorylation & Shotgun proteomics. The author has an hindex of 37, co-authored 57 publications receiving 6073 citations. Previous affiliations of Amy-Joan L. Ham include Veterans Health Administration & Belmont University.
Papers
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Broad Institute1, Buck Institute for Research on Aging2, Harvard University3, National Institute of Standards and Technology4, Texas A&M University5, Vanderbilt University6, University of California, San Francisco7, University of Victoria8, Purdue University9, New York University10, National Institutes of Health11, University of North Carolina at Chapel Hill12, Indiana University13, Fred Hutchinson Cancer Research Center14, Memorial Sloan Kettering Cancer Center15
TL;DR: A multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC demonstrates that these assays can be highly reproducible within and across laboratories and instrument platforms.
Abstract: Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low mug/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.
997 citations
TL;DR: It is shown that oxidation of paired regulatory domain methionine residues sustains CaMKII activity in the absence of Ca2+/CaM and highlights the critical importance of oxidation-dependent CaMK II activation to AngII and ischemic myocardial apoptosis.
989 citations
Vanderbilt University1, Texas A&M University2, National Institute of Standards and Technology3, Memorial University of Newfoundland4, University of Arizona5, Broad Institute6, New York University7, Merck & Co.8, Purdue University9, Buck Institute for Research on Aging10, Fred Hutchinson Cancer Research Center11, University of California, San Francisco12, National Institutes of Health13, Memorial Sloan Kettering Cancer Center14
TL;DR: The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides.
Abstract: The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproduci...
504 citations
TL;DR: A comprehensive proteomic analysis of exosomes from parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRas allele only), showing Mutant KRAS status dramatically affects the composition of the exosome proteome.
459 citations
TL;DR: The use of commercially available microcentrifugation devices (spin filters) for cleanup and digestion of protein samples for mass spectrometry analyses provides digestion efficiencies comparable to standard in‐solution digests, avoids lengthy dialysis steps, and allows rapid cleanup of samples containing salts, some detergents, and acidic or basic buffers.
Abstract: We describe the use of commercially available microcentrifugation devices (spin filters) for cleanup and digestion of protein samples for mass spectrometry analyses. The protein sample is added to the upper chamber of a spin filter with a > or = 3000 molecular weight cutoff membrane and then washed prior to resuspension in ammonium bicarbonate. The protein is then reduced, alkylated, and digested with trypsin in the upper chamber and the peptides are recovered by centrifugation through the membrane. The method provides digestion efficiencies comparable to standard in-solution digests, avoids lengthy dialysis steps, and allows rapid cleanup of samples containing salts, some detergents, and acidic or basic buffers.
364 citations
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TL;DR: Exosomes were described as vesicles of endosomal origin secreted from reticulocytes in the 1980s as discussed by the authors, and their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.
Abstract: In the 1980s, exosomes were described as vesicles of endosomal origin secreted from reticulocytes. Interest increased around these extracellular vesicles, as they appeared to participate in several cellular processes. Exosomes bear proteins, lipids, and RNAs, mediating intercellular communication between different cell types in the body, and thus affecting normal and pathological conditions. Only recently, scientists acknowledged the difficulty of separating exosomes from other types of extracellular vesicles, which precludes a clear attribution of a particular function to the different types of secreted vesicles. To shed light into this complex but expanding field of science, this review focuses on the definition of exosomes and other secreted extracellular vesicles. Their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.
3,959 citations
TL;DR: The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM).
Abstract: Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
3,794 citations
01 Jan 2014
TL;DR: The definition of exosomes and other secreted extracellular vesicles, which mediating intercellular communication between different cell types in the body, and thus affecting normal and pathological conditions are focused on.
Abstract: In the 1980s, exosomes were described as vesicles of endosomal origin secreted from reticulocytes. Interest increased around these extracellular vesicles, as they appeared to participate in several cellular processes. Exosomes bear proteins, lipids, and RNAs, mediating intercellular communication between different cell types in the body, and thus affecting normal and pathological conditions. Only recently, scientists acknowledged the difficulty of separating exosomes from other types of extracellular vesicles, which precludes a clear attribution of a particular function to the different types of secreted vesicles. To shed light into this complex but expanding field of science, this review focuses on the definition of exosomes and other secreted extracellular vesicles. Their biogenesis, their secretion, and their subsequent fate are discussed, as their functions rely on these important processes.
3,321 citations
Icahn School of Medicine at Mount Sinai1, University of Michigan2, Pasteur Institute3, University of California, San Francisco4, European Bioinformatics Institute5, University of California, San Diego6, University of North Carolina at Chapel Hill7, Fred Hutchinson Cancer Research Center8, Gladstone Institutes9, Buck Institute for Research on Aging10
TL;DR: A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.
Abstract: A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein–protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19. A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.
3,319 citations
European Bioinformatics Institute1, Institute for Systems Biology2, University of California, San Diego3, Swiss Institute of Bioinformatics4, Ruhr University Bochum5, University of Cambridge6, University of California, San Francisco7, Wiley-VCH8, Spanish National Research Council9, Ghent University10, University of Liverpool11
TL;DR: The PX submission tool simplifies the process of submitting data to PRIDE by automating the very labor-intensive and therefore time-heavy and expensive process of manually downloading and editing files.
Abstract: 5. Tools available and ways to submit data to PX ............................................................. 11 5.1. MS/MS data submissions to PRIDE .................................................................................... 11 5.1.1. Creation of supported files for “Complete” submissions .................................................. 11 5.1.1.1. PRIDE XML .................................................................................................................................. 11 5.1.1.2. mzIdentML ................................................................................................................................. 13 5.1.2. Checking the files before submission (initial quality assessment) ..................................... 14 5.1.3. File submission to PRIDE: the PX submission tool ............................................................. 15 5.1.3.1. General Information ................................................................................................................... 15 5.1.3.2. Functionality, Design and Implementation Details .................................................................... 15 5.1.3.3. New open source libraries made available with PX submission tool ......................................... 18 5.1.3.4. PX Submission Tool Java Web Start ............................................................................................ 18 5.1.4. File submission to PRIDE: Command line support using Aspera ........................................ 19 5.1.5. Examples of Partial submissions to PRIDE ......................................................................... 19 5.2. SRM data submissions via PASSEL ..................................................................................... 20
2,436 citations