The GXXXG motif is a frequently occurring sequence of residues that is known to favor helix-helix... more The GXXXG motif is a frequently occurring sequence of residues that is known to favor helix-helix interactions in membrane proteins. Here we show that the GXXXG motif is also prevalent in soluble proteins whose structures have been determined. Some 152 proteins from a nonredundant PDB set contain at least one R-helix with the GXXXG motif, 41 ( 9% more than
We combine mathematical modeling with experiments in living mice to quantify the relative roles o... more We combine mathematical modeling with experiments in living mice to quantify the relative roles of intrinsic cellular vs. tissue-scale physiological contributors to chemotherapy drug resistance, which are difficult to understand solely through experimentation. Experiments in cell culture and in mice with drug-sensitive (Eµ-myc/Arf-/-) and drug-resistant (Eµ-myc/p53-/-) lymphoma cell lines were conducted to calibrate and validate a mechanistic mathematical model. Inputs to inform the model include tumor drug transport characteristics, such as blood volume fraction, average geometric mean blood vessel radius, drug diffusion penetration distance, and drug response incell culture. Model results show that the drug response in mice, represented by the fraction of dead tumor volume, can be reliably predicted from these inputs. Hence, a proof-ofprinciple for predictive quantification of lymphoma drug therapy was established based on both cellular and tissue-scale physiological contributions. We further demonstrate that, if the in vitro cytotoxic response of a specific cancer cell line under chemotherapy is known, the model is then able to predict the treatment efficacy in vivo. Lastly, tissue blood volume fraction was determined to be the most sensitive model parameter and a primary contributor to drug resistance.
Protein engineering, design & selection : PEDS, Jan 19, 2015
Phage display libraries of human single-chain variable fragments (scFvs) are a reliable source of... more Phage display libraries of human single-chain variable fragments (scFvs) are a reliable source of fully human antibodies for scientific and clinical applications. Frequently, scFvs form the basis of larger, bivalent formats to increase valency and avidity. A small and versatile bivalent antibody fragment is the diabody, a cross-paired scFv dimer (∼55 kDa). However, generation of diabodies from selected scFvs requires decreasing the length of the interdomain scFv linker, typically by overlap PCR. To simplify this process, we designed two scFv linkers with integrated restriction sites for easy linker length reduction (17-residue to 7-residue or 18-residue to 5-residue, respectively) and generated two fully human scFv phage display libraries. The larger library (9 × 10(9) functional members) was employed for selection against a model antigen, human N-cadherin, yielding novel scFv clones with low nanomolar monovalent affinities. ScFv clones from both libraries were reformatted into diab...
Cardinal is an R package for statistical analysis of mass spectrometry-based imaging (MSI) experi... more Cardinal is an R package for statistical analysis of mass spectrometry-based imaging (MSI) experiments of biological samples such as tissues. Cardinal supports both MALDI and DESI-based IMS workflows, and experiments with multiple tissues and complex designs. The main analytical functionalities include (1) image segmentation, which partitions a tissue into regions of homogeneous chemical composition, selects the number of segments and the subset of informative ions, and characterizes the associated uncertainty, and (2) image classification, which assigns locations on the tissue to pre-defined classes, selects the subset of informative ions, and estimates the resulting classification error by (cross-) validation. The statistical methods are based on mixture modeling and regularization. The code, the documentation, and examples are available open-source at www.cardinalmsi.org under the Artistic-2.0 license. The package is available at www.bioconductor.org. [email protected].
AKT has a critical role in relaying cell survival and proliferation signals initiated by ligand b... more AKT has a critical role in relaying cell survival and proliferation signals initiated by ligand binding to surface receptors in mammalian cells. Induction of AKT serine/threonine kinase activity is augmented by the T-cell leukemia-1 (TCL1) oncoprotein through a physical association requiring the AKT pleckstrin homology domain. Here, we used molecular modeling and identified an exposed hydrophobic patch composed of two discontinuous amino acid stretches near one end of the TCL1 -barrel that was required for a TCL1-AKT association. Site-directed mutations of this region did not affect TCL1 secondary structure, yet they disrupted interactions with AKT. This region was found in other members of the TCL1 oncoprotein family, such as TCL1b and MTCP1, and suggested a conserved, novel AKT binding domain. Interestingly, TCL1 and AKT co-localize in multiple cell compartments, but only extracts from the plasma membrane stimulate optimal complex formation in vitro. Identification of an AKT binding domain on TCL1 is an important step in deciphering the complex interactions that regulate AKT kinase activity in lymphocyte development and neoplasia within the immune system. † This work was supported by an Amgen/UC BioStar Award (S98-35 to M.A.T.), a UCLA CFAR Award (S.W.F. and M.A.T.), the Lymphoma Research Foundation of America (M.A.T.), a PHSNS Award (T32-CA09056 to C.S.M.), and the National Institutes of Health (GM40185 to P.M. and CA74929 to M.A.T.).
Genome Biology 2006, 7:R106 comment reviews reports deposited research refereed research interact... more Genome Biology 2006, 7:R106 comment reviews reports deposited research refereed research interactions information
Mass spectrometry-based quantitative proteomics has become an important component of biological a... more Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using 4600,000 peptide identifications generated by four proteomic platforms, we empirically identified 416,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with 485% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation).
A crucial aim upon the completion of the human genome is the verification and functional annotati... more A crucial aim upon the completion of the human genome is the verification and functional annotation of all predicted genes and their protein products. Here we describe the mapping of peptides derived from accurate interpretations of protein tandem mass spectrometry (MS) data to eukaryotic genomes and the generation of an expandable resource for integration of data from many diverse proteomics experiments. Furthermore, we demonstrate that peptide identifications obtained from high-throughput proteomics can be integrated on a large scale with the human genome. This resource could serve as an expandable repository for MS-derived proteome information.
Distance constraints in proteins and protein complexes provide invaluable information for calcula... more Distance constraints in proteins and protein complexes provide invaluable information for calculation of 3D structures, identification of protein binding partners and localization of protein-protein contact sites. We have developed an integrative approach to identify and characterize such sites through the analysis of proteolytic products derived from proteins chemically cross-linked by isotopically coded cross-linkers using LC-MALDI tandem mass spectrometry and computer
Yeast strain growth, a-factor synchronization, release and collection were performed as described... more Yeast strain growth, a-factor synchronization, release and collection were performed as described previously , and cell aliquots for this study and for analysis of translation state
The identification of the enzymes involved in the metabolism of simple and complex carbohydrates ... more The identification of the enzymes involved in the metabolism of simple and complex carbohydrates presents one bioinformatic challenge in the post-genomic era. Here, we present the PFIT and PFRIT algorithms for identifying those proteins adopting the ␣/ barrel fold that function as glycosidases. These algorithms are based on the observation that proteins adopting the ␣/ barrel fold share positions in their tertiary structures having equivalent sets of atomic interactions. These are conserved tertiary interaction positions, which have been implicated in both structure and function. Glycosidases adopting the ␣/ barrel fold share more conserved tertiary interactions than ␣/ barrel proteins having other functions. The enrichment pattern of conserved tertiary interactions in the glycosidases is the information that PFIT and PFRIT use to predict whether any given ␣/ barrel will function as a glycosidase or not. Using as a test set a database of 19 glycosidase and 45 nonglycosidase ␣/ barrel proteins with low sequence similarity, PFIT and PFRIT can correctly predict glycosidase function for 84% of the proteins known to function as glycosidases. PFIT and PFRIT incorrectly predict glycosidase function for 25% of the nonglycosidases. The program PSI-BLAST can also correctly identify 84% of the 19 glycosidases, however, it incorrectly predicts glycosidase function for 50% of the nonglycosidases (twofold greater than PFIT and PFRIT). Overall, we demonstrate that the structure-based PFIT and PFRIT algorithms are both more selective and sensitive for predicting glycosidase function than the sequence-based PSI-BLAST algorithm.
Proceedings of the National Academy of Sciences, 2002
The Directional Atomic Solvation EnergY (DASEY) is an atom-based description of the environment o... more The Directional Atomic Solvation EnergY (DASEY) is an atom-based description of the environment of an amino acid position within a known 3D protein structure. The DASEY has been developed to align and score a probe amino acid sequence to a library of template protein structures for fold assignment. DASEY is computed by summing the atomic solvation parameters of atoms falling within a tetrahedral sector, or petal, extending 16 A along each of the four bond axes of each alpha-carbon atom of the protein. The DASEY discriminates between pairs of structurally equivalent positions and random pairs in protein structures sharing a fold but belonging to different superfamilies, unlike some previous descriptors of protein environments, such as buried area. Furthermore, the DASEY values have characteristic patterns of residue replacement, an essential feature of a successful fold assignment method. Benchmarking fold assignment with DASEY achieves coverage of 56% of sequences with 90% accuracy when probe sequences are matched to protein structural templates belonging to the same fold but to a different superfamily, an improvement of greater than 200% over a previous method.
Proceedings of the National Academy of Sciences, 2000
Pyrobaculum Genome. Predicted coding region sequences of the PA genome were obtained from the Jef... more Pyrobaculum Genome. Predicted coding region sequences of the PA genome were obtained from the Jeffrey H. Miller Laboratory of the University of California Los Angeles Molecular Biology Institute and correspond to the 1͞1͞99 version of the genome. This version contained 2,681 open reading frames (ORFs) predicted to code for proteins. Membrane-Spanning Proteins. Of the 2,681 PA ORFs, 551 contained membrane-spanning ␣-helices as determined by MOMENT (7) (PAHOME͞TRANSMEMBRANEHELIX PREDICTIONRESULTS). These proteins were excluded from fold recognition and novel fold prediction analysis. Protein Sequence Databases. The Online Mendelian Inheritance in Man (OMIM) database containing 15,743 sequences was downloaded from the National Center for Biotechnology Information (http:͞͞www.ncbi.nlm.nih.gov͞Omim͞; authored and edited by V. A. McKusick and his colleagues at Johns Hopkins and elsewhere). Similarity searches of the OMIM database were performed by using a local implementation of the Smith-Waterman algorithm (8) with probability values determined by Waterman-Vingron statistics (9, 10).
Proceedings of the National Academy of Sciences, 2002
Disulfide bonds have only rarely been found in intracellular proteins. That pattern is consistent... more Disulfide bonds have only rarely been found in intracellular proteins. That pattern is consistent with the chemically reducing environment inside the cells of well-studied organisms. However, recent experiments and new calculations based on genomic data of archaea provide striking contradictions to this pattern. Our results indicate that the intracellular proteins of certain hyperthermophilic archaea, especially the crenarchaea Pyrobaculum aerophilum and Aeropyrum pernix, are rich in disulfide bonds. This finding implicates disulfide bonding in stabilizing many thermostable proteins and points to novel chemical environments inside these microbes. These unexpected results illustrate the wealth of biochemical insights available from the growing reservoir of genomic data.
The completion of the sequencing of the human genome and the concurrent, rapid development of hig... more The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. Peptide-Atlas (http://www.peptideatlas.org/) addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.
| Technologies for genome-wide analyses typically undergo a transition from a discovery phase to ... more | Technologies for genome-wide analyses typically undergo a transition from a discovery phase to a scoring phase. In the discovery phase, the genomic universe is explored and all pertinent data are noted. In the scoring phase, relevant entities are screened to reveal groups of genes that are associated with specific biological processes or conditions. In this article, we propose that the transition from a discovery to a scoring phase is also essential, feasible and imminent for proteomics.
Objective Scope Example Approach Discovery of new entities Broad scale Focused Comprehensive Glob... more Objective Scope Example Approach Discovery of new entities Broad scale Focused Comprehensive Global Selected Assay for known entities Restrictive or targeted Proteomics Expression profiling HUPO PPP PTM discovery Protein complexes Biomarker candidate verification SRM or MRM Peptide quantification Peptide sequencing, database searching Peptide identification and quantification
The GXXXG motif is a frequently occurring sequence of residues that is known to favor helix-helix... more The GXXXG motif is a frequently occurring sequence of residues that is known to favor helix-helix interactions in membrane proteins. Here we show that the GXXXG motif is also prevalent in soluble proteins whose structures have been determined. Some 152 proteins from a nonredundant PDB set contain at least one R-helix with the GXXXG motif, 41 ( 9% more than
We combine mathematical modeling with experiments in living mice to quantify the relative roles o... more We combine mathematical modeling with experiments in living mice to quantify the relative roles of intrinsic cellular vs. tissue-scale physiological contributors to chemotherapy drug resistance, which are difficult to understand solely through experimentation. Experiments in cell culture and in mice with drug-sensitive (Eµ-myc/Arf-/-) and drug-resistant (Eµ-myc/p53-/-) lymphoma cell lines were conducted to calibrate and validate a mechanistic mathematical model. Inputs to inform the model include tumor drug transport characteristics, such as blood volume fraction, average geometric mean blood vessel radius, drug diffusion penetration distance, and drug response incell culture. Model results show that the drug response in mice, represented by the fraction of dead tumor volume, can be reliably predicted from these inputs. Hence, a proof-ofprinciple for predictive quantification of lymphoma drug therapy was established based on both cellular and tissue-scale physiological contributions. We further demonstrate that, if the in vitro cytotoxic response of a specific cancer cell line under chemotherapy is known, the model is then able to predict the treatment efficacy in vivo. Lastly, tissue blood volume fraction was determined to be the most sensitive model parameter and a primary contributor to drug resistance.
Protein engineering, design & selection : PEDS, Jan 19, 2015
Phage display libraries of human single-chain variable fragments (scFvs) are a reliable source of... more Phage display libraries of human single-chain variable fragments (scFvs) are a reliable source of fully human antibodies for scientific and clinical applications. Frequently, scFvs form the basis of larger, bivalent formats to increase valency and avidity. A small and versatile bivalent antibody fragment is the diabody, a cross-paired scFv dimer (∼55 kDa). However, generation of diabodies from selected scFvs requires decreasing the length of the interdomain scFv linker, typically by overlap PCR. To simplify this process, we designed two scFv linkers with integrated restriction sites for easy linker length reduction (17-residue to 7-residue or 18-residue to 5-residue, respectively) and generated two fully human scFv phage display libraries. The larger library (9 × 10(9) functional members) was employed for selection against a model antigen, human N-cadherin, yielding novel scFv clones with low nanomolar monovalent affinities. ScFv clones from both libraries were reformatted into diab...
Cardinal is an R package for statistical analysis of mass spectrometry-based imaging (MSI) experi... more Cardinal is an R package for statistical analysis of mass spectrometry-based imaging (MSI) experiments of biological samples such as tissues. Cardinal supports both MALDI and DESI-based IMS workflows, and experiments with multiple tissues and complex designs. The main analytical functionalities include (1) image segmentation, which partitions a tissue into regions of homogeneous chemical composition, selects the number of segments and the subset of informative ions, and characterizes the associated uncertainty, and (2) image classification, which assigns locations on the tissue to pre-defined classes, selects the subset of informative ions, and estimates the resulting classification error by (cross-) validation. The statistical methods are based on mixture modeling and regularization. The code, the documentation, and examples are available open-source at www.cardinalmsi.org under the Artistic-2.0 license. The package is available at www.bioconductor.org. [email protected].
AKT has a critical role in relaying cell survival and proliferation signals initiated by ligand b... more AKT has a critical role in relaying cell survival and proliferation signals initiated by ligand binding to surface receptors in mammalian cells. Induction of AKT serine/threonine kinase activity is augmented by the T-cell leukemia-1 (TCL1) oncoprotein through a physical association requiring the AKT pleckstrin homology domain. Here, we used molecular modeling and identified an exposed hydrophobic patch composed of two discontinuous amino acid stretches near one end of the TCL1 -barrel that was required for a TCL1-AKT association. Site-directed mutations of this region did not affect TCL1 secondary structure, yet they disrupted interactions with AKT. This region was found in other members of the TCL1 oncoprotein family, such as TCL1b and MTCP1, and suggested a conserved, novel AKT binding domain. Interestingly, TCL1 and AKT co-localize in multiple cell compartments, but only extracts from the plasma membrane stimulate optimal complex formation in vitro. Identification of an AKT binding domain on TCL1 is an important step in deciphering the complex interactions that regulate AKT kinase activity in lymphocyte development and neoplasia within the immune system. † This work was supported by an Amgen/UC BioStar Award (S98-35 to M.A.T.), a UCLA CFAR Award (S.W.F. and M.A.T.), the Lymphoma Research Foundation of America (M.A.T.), a PHSNS Award (T32-CA09056 to C.S.M.), and the National Institutes of Health (GM40185 to P.M. and CA74929 to M.A.T.).
Genome Biology 2006, 7:R106 comment reviews reports deposited research refereed research interact... more Genome Biology 2006, 7:R106 comment reviews reports deposited research refereed research interactions information
Mass spectrometry-based quantitative proteomics has become an important component of biological a... more Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using 4600,000 peptide identifications generated by four proteomic platforms, we empirically identified 416,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with 485% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation).
A crucial aim upon the completion of the human genome is the verification and functional annotati... more A crucial aim upon the completion of the human genome is the verification and functional annotation of all predicted genes and their protein products. Here we describe the mapping of peptides derived from accurate interpretations of protein tandem mass spectrometry (MS) data to eukaryotic genomes and the generation of an expandable resource for integration of data from many diverse proteomics experiments. Furthermore, we demonstrate that peptide identifications obtained from high-throughput proteomics can be integrated on a large scale with the human genome. This resource could serve as an expandable repository for MS-derived proteome information.
Distance constraints in proteins and protein complexes provide invaluable information for calcula... more Distance constraints in proteins and protein complexes provide invaluable information for calculation of 3D structures, identification of protein binding partners and localization of protein-protein contact sites. We have developed an integrative approach to identify and characterize such sites through the analysis of proteolytic products derived from proteins chemically cross-linked by isotopically coded cross-linkers using LC-MALDI tandem mass spectrometry and computer
Yeast strain growth, a-factor synchronization, release and collection were performed as described... more Yeast strain growth, a-factor synchronization, release and collection were performed as described previously , and cell aliquots for this study and for analysis of translation state
The identification of the enzymes involved in the metabolism of simple and complex carbohydrates ... more The identification of the enzymes involved in the metabolism of simple and complex carbohydrates presents one bioinformatic challenge in the post-genomic era. Here, we present the PFIT and PFRIT algorithms for identifying those proteins adopting the ␣/ barrel fold that function as glycosidases. These algorithms are based on the observation that proteins adopting the ␣/ barrel fold share positions in their tertiary structures having equivalent sets of atomic interactions. These are conserved tertiary interaction positions, which have been implicated in both structure and function. Glycosidases adopting the ␣/ barrel fold share more conserved tertiary interactions than ␣/ barrel proteins having other functions. The enrichment pattern of conserved tertiary interactions in the glycosidases is the information that PFIT and PFRIT use to predict whether any given ␣/ barrel will function as a glycosidase or not. Using as a test set a database of 19 glycosidase and 45 nonglycosidase ␣/ barrel proteins with low sequence similarity, PFIT and PFRIT can correctly predict glycosidase function for 84% of the proteins known to function as glycosidases. PFIT and PFRIT incorrectly predict glycosidase function for 25% of the nonglycosidases. The program PSI-BLAST can also correctly identify 84% of the 19 glycosidases, however, it incorrectly predicts glycosidase function for 50% of the nonglycosidases (twofold greater than PFIT and PFRIT). Overall, we demonstrate that the structure-based PFIT and PFRIT algorithms are both more selective and sensitive for predicting glycosidase function than the sequence-based PSI-BLAST algorithm.
Proceedings of the National Academy of Sciences, 2002
The Directional Atomic Solvation EnergY (DASEY) is an atom-based description of the environment o... more The Directional Atomic Solvation EnergY (DASEY) is an atom-based description of the environment of an amino acid position within a known 3D protein structure. The DASEY has been developed to align and score a probe amino acid sequence to a library of template protein structures for fold assignment. DASEY is computed by summing the atomic solvation parameters of atoms falling within a tetrahedral sector, or petal, extending 16 A along each of the four bond axes of each alpha-carbon atom of the protein. The DASEY discriminates between pairs of structurally equivalent positions and random pairs in protein structures sharing a fold but belonging to different superfamilies, unlike some previous descriptors of protein environments, such as buried area. Furthermore, the DASEY values have characteristic patterns of residue replacement, an essential feature of a successful fold assignment method. Benchmarking fold assignment with DASEY achieves coverage of 56% of sequences with 90% accuracy when probe sequences are matched to protein structural templates belonging to the same fold but to a different superfamily, an improvement of greater than 200% over a previous method.
Proceedings of the National Academy of Sciences, 2000
Pyrobaculum Genome. Predicted coding region sequences of the PA genome were obtained from the Jef... more Pyrobaculum Genome. Predicted coding region sequences of the PA genome were obtained from the Jeffrey H. Miller Laboratory of the University of California Los Angeles Molecular Biology Institute and correspond to the 1͞1͞99 version of the genome. This version contained 2,681 open reading frames (ORFs) predicted to code for proteins. Membrane-Spanning Proteins. Of the 2,681 PA ORFs, 551 contained membrane-spanning ␣-helices as determined by MOMENT (7) (PAHOME͞TRANSMEMBRANEHELIX PREDICTIONRESULTS). These proteins were excluded from fold recognition and novel fold prediction analysis. Protein Sequence Databases. The Online Mendelian Inheritance in Man (OMIM) database containing 15,743 sequences was downloaded from the National Center for Biotechnology Information (http:͞͞www.ncbi.nlm.nih.gov͞Omim͞; authored and edited by V. A. McKusick and his colleagues at Johns Hopkins and elsewhere). Similarity searches of the OMIM database were performed by using a local implementation of the Smith-Waterman algorithm (8) with probability values determined by Waterman-Vingron statistics (9, 10).
Proceedings of the National Academy of Sciences, 2002
Disulfide bonds have only rarely been found in intracellular proteins. That pattern is consistent... more Disulfide bonds have only rarely been found in intracellular proteins. That pattern is consistent with the chemically reducing environment inside the cells of well-studied organisms. However, recent experiments and new calculations based on genomic data of archaea provide striking contradictions to this pattern. Our results indicate that the intracellular proteins of certain hyperthermophilic archaea, especially the crenarchaea Pyrobaculum aerophilum and Aeropyrum pernix, are rich in disulfide bonds. This finding implicates disulfide bonding in stabilizing many thermostable proteins and points to novel chemical environments inside these microbes. These unexpected results illustrate the wealth of biochemical insights available from the growing reservoir of genomic data.
The completion of the sequencing of the human genome and the concurrent, rapid development of hig... more The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. Peptide-Atlas (http://www.peptideatlas.org/) addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.
| Technologies for genome-wide analyses typically undergo a transition from a discovery phase to ... more | Technologies for genome-wide analyses typically undergo a transition from a discovery phase to a scoring phase. In the discovery phase, the genomic universe is explored and all pertinent data are noted. In the scoring phase, relevant entities are screened to reveal groups of genes that are associated with specific biological processes or conditions. In this article, we propose that the transition from a discovery to a scoring phase is also essential, feasible and imminent for proteomics.
Objective Scope Example Approach Discovery of new entities Broad scale Focused Comprehensive Glob... more Objective Scope Example Approach Discovery of new entities Broad scale Focused Comprehensive Global Selected Assay for known entities Restrictive or targeted Proteomics Expression profiling HUPO PPP PTM discovery Protein complexes Biomarker candidate verification SRM or MRM Peptide quantification Peptide sequencing, database searching Peptide identification and quantification
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Papers by Parag Mallick