A5054016623- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Analytical chemistry methods development
- Analytical Chemistry and Chromatography
- Electrochemical Analysis and Applications
- Ion-surface interactions and analysis
- Cellular transport and secretion
- Protein purification and stability
- Laser-induced spectroscopy and plasma
- Genetics, Aging, and Longevity in Model Organisms
- Enzyme Structure and Function
- Neuroendocrine regulation and behavior
- Chemical Synthesis and Analysis
- Pesticide Residue Analysis and Safety
- Cancer Mechanisms and Therapy
- Protein Degradation and Inhibitors
- Click Chemistry and Applications
- Fungal and yeast genetics research
- Synthesis and Biological Evaluation
- Molecular Biology Techniques and Applications
- Identification and Quantification in Food
- Neonatal Respiratory Health Research
- Nuclear Physics and Applications
- Biotin and Related Studies
Genomics Institute of the Novartis Research Foundation
2007-2022
Scripps Research Institute
2002-2015
Technical University of Denmark
2008
Salk Institute for Biological Studies
2007
University of California, San Diego
2007
The University of Texas at Austin
2000-2002
ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases has been developed. This uses three tier scoring scheme. First, binomial probability is used as preliminary scheme to select candidate peptides. The scores generated by ProLuCID minimize molecular weight bias are independent of database size. A modified cross-correlation score calculated each identified the probability. function models isotopic distributions fragment ions...
Abstract As the speed with which proteomic labs generate data increases along scale of projects they are undertaking, resulting storage and processing problems will continue to challenge computational resources. This is especially true for shotgun techniques that can tens thousands spectra per instrument each day. One design factor leading many these caused by storing database identifications a given spectrum as individual files. While be addressed all search results in large relational...
DAF-2, an insulin receptor-like protein, regulates metabolism, development, and aging in Caenorhabditis elegans. In a quantitative proteomic study, we identified 86 proteins that were more or less abundant long-lived daf-2 mutant worms than wild-type worms. Genetic studies on subset of these indicated they act one processes regulated by including entry into the dauer developmental stage aging. particular, discovered compensatory mechanism activated response to reduced DAF-2 signaling, which...
We previously reported the metabolic 15N labeling of a rat where enrichment ranged from 94% to 74%. report here an improved strategy which generates throughout all tissues rat. A high internal standard is necessary for accurate quantitation, and thus, this approach will allow quantitative mass spectrometry analysis animal models disease targeting any tissue.
Both in vivo data preclinical cancer models and vitro with T cells from patients advanced support a role for Tim-3 blockade promoting effective anti-tumor immunity. Consequently, there is considerable interest the clinical development of antibody-based therapeutics that target immunotherapy. A challenge to this fact several ligands have been identified: galectin-9, phosphatidylserine, HMGB1, most recently, CEACAM1. These observations raise important question which these multiple...
Multidimensional separation is one of the most successful approaches for proteomics studies that deal with complex samples. We have developed an automated ultra-high-pressure multidimensional liquid chromatography system operates up to ∼20 kpsi improve separations and increase protein coverage from limited amount The reversed-phase gradient operated in constant-flow mode opposed constant-pressure mode, which typical previous systems. In contrast systems, shape fully controllable can be...
The quantitative proteomic analysis of complex protein mixtures is emerging as a technically challenging but viable systems-level approach for studying cellular function. This study presents large-scale comparative abundances from yeast lysates derived both wild-type and strains lacking key components the Snf1 kinase complex. Four different were grown under well-controlled chemostat conditions. Multidimensional identification technology followed by quantitation using either spectral counting...
Large-scale proteomic analysis of the mammalian brain has been successfully performed with mass spectrometry techniques, such as Multidimensional Protein Identification Technology (MudPIT), to identify hundreds thousands proteins. Strategies efficiently quantify protein expression levels in a large-scale fashion, however, are lacking. Here, we demonstrate novel quantification strategy for proteomics called SILAM (Stable Isotope Labeling Mammals). We utilized (15)N metabolically labeled rat...
Protein phosphorylation has become a focus of many proteomic studies due to the central role that it plays in biology. We combine peptide-based gel-free isoelectric focusing and immobilized metal affinity chromatography enhance detection events within complex protein samples using LC−MS. This method is then used carry out quantitative phosphoproteomic analysis tumor necrosis factor (TNF) pathway HeLa cells metabolically labeled with 15N-containing amino acids, where 145 sites were found be...
Hydrogen–deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein–ligand interactions, protein folding, and dynamics. However, HDX-MS still emergent quality control of biopharmaceuticals establishing dynamic similarity between a biosimilar innovator therapeutic. Because industry will conduct measurements over product lifetime in multiple locations, understanding reproducibility critical. To determine the continuous-labeling, bottom-up...
Tristetraprolin (TTP) is a zinc-finger protein that binds to AREs (AU-rich elements) within certain mRNAs and causes destabilization of those mRNAs. Mice deficient in TTP develop profound inflammatory syndrome with erosive arthritis, autoimmunity myeloid hyperplasia. Previous studies showed phosphorylated extensively intact cells. However, limited information available about the identities these phosphorylation sites. We investigated sites human from transfected HEK-293 cells by MS...
The quantitative analysis of complex biological samples has emerged as a key research area in the field proteomics. Although proteomic experiments remain challenging, these strategies have been greatly facilitated by development newer high-performance mass spectrometers. In this work, we evaluated use LTQ-Orbitrap, hybrid spectrometer which linear ion trap is coupled to an Orbitrap analyzer, for analyses. By analyzing range yeast protein standards, found that high accuracy, resolution, large...
We investigated and compared three approaches for shotgun protein identification by combining MS MS/MS information using LTQ-Orbitrap high mass accuracy data. In the first approach, we employed a unique identifier method where peaks matched to peptides predicted from proteins identified an database search are subtracted before as identifiers identification. second method, used accurate time tag building potential retention previous MudPIT analyses. For third peptide fingerprinting-like...
Amide hydrogen/deuterium exchange is a commonly used technique for studying the dynamics of proteins and their interactions with other or ligands. When coupled liquid chromatography mass spectrometry, provides several unique advantages over structural characterization techniques including very high sensitivity, ability to analyze in complex environments, large range. A fundamental limitation arises from loss deuterium label (back-exchange) during course analysis. method limit separation...
Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation the wealth data generated by HX-MS experiments as well other methods would greatly benefit from availability predictions derived structures or models comparison with experiment. Most reported computational modeling employed...
Peptide identification based on tandem mass spectrometry and database searching algorithms has become one of the central technologies in proteomics. At heart this technology is ability to reproducibly acquire high-quality spectra for interrogation. The variability generation often assumed be minimal, peptide identifications are typically a single spectrum. In paper, we characterize variance scores derived from replicate using several search demonstrate effects spectral correct peptides. We...
We evaluate the effect of ion-abundance threshold settings for data-dependent acquisition on a hybrid LTQ-Orbitrap mass spectrometer, analyzing features such as total number spectra collected, signal to noise ratio full MS scans, spectral quality tandem acquired, and peptides proteins identified from complex mixture. find that increasing generally decreases quantity but increases acquired. This is especially true when setting set above level scan. compare two distinct experimental...
We have developed an approach to identify the molecular weight of a peptide ion directly from its corresponding tandem mass spectrum using cross-correlation function. shown that monoisotopic can be calculated for ∼90% spectra identified tryptic digests complex protein mixtures. The accuracy masses was dependent on resolution and analyzed, but typically <0.25 amu linear trap spectra. ability calculate accurate weights low-resolution data should significantly improve both speed performance...
A mathematical solution and an experimental procedure are described for calculating the maximum number of transient signals, such as those obtained using ETV sample introduction into ICPMS, that can be monitored by a scanning spectrometer, quadrupole mass analyzer. The total masses per firing is shown to dependent on values chosen data collection (i.e., scan time dwell time) necessary limits detection required method. theory shows effect statistical noise, peak shapes, inconsistent...