What is protein profiling?

The detection of the character and quantity of specific sets of proteins in blood or other specimens. Protein profiling has been used as a means of diagnosing specific illnesses, esp. cancers or infectious diseases known to release unique protein patterns into serum.

Listen to pronunciation. (PROH-tee-OH-mik PROH-file) Information about all proteins that are made in blood, other body fluids, or tissues, at certain times. A proteomic profile may be used to find and diagnose a disease or condition and to see how well the body responds to treatment.

Over the past 10 years, activity-based protein profiling (ABPP) is increasingly used in plant science. ABPP monitors the activities of hundreds of plant proteins using tagged chemical probes that react with the active site of proteins in a mechanism-dependent manner.

Activity-based protein profiling (ABPP) is a chemical proteomics approach that utilizes small-molecule probes to determine the functional state of enzymes directly in native systems. … ABPP probes have been developed that react selectively with most members of specific enzyme classes.

Finally, profile–profile alignment is used to search databases of profiles, usually derived from sequences of known structure in the PDB, and to produce accurate sequence–structure alignments of the query sequence and template structure.

Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. … Several software implementations and two large libraries of profile HMMs of common protein domains are available.

Definition. Genomics is the study of genomes which refers to the complete set of genes or genetic material present in a cell or organism. Proteomics is the branch of molecular biology that studies the set of proteins expressed by the genome of an organism.

Proteomics is the large-scale study of the structure and function of proteins. In its strictest sense, the word “proteome” refers to the set of proteins encoded by the genome, including the added variation of posttranslational modification.

The importance of the proteome cannot be overstated as it is the proteins within the cell that provide structure, produce energy, as well as allow communication, movement, and reproduction. Basically, proteins provide structural and functional framework for cellular life.

A pattern is thus a qualitative description of a motif in terms of amino acid sequence. The concept of a profile extends this concept, allowing a quantitative description of a motif, by assigning probabilities to the occurrence of a particular amino acid at each position of a motif.

What is a database profile? A database profile is a named set of parameters stored in your system registry that defines a connection to a particular database in the InfoMaker development environment. You must create a database profile for each data connection.

Position-Specific Iterative (PSI)-BLAST is a protein sequence profile search method that builds off the alignments generated by a run of the BLASTp program. … This process is iteratively continued until desired or until convergence, i.e., the state where no new sequences are detected above the defined threshold.

A protein database is one or more datasets about proteins, which could include a protein’s amino acid sequence, conformation, structure, and features such as active sites. Protein databases are compiled by the translation of DNA sequences from different gene databases and include structural information.

Protein motifs are small regions of protein three-dimensional structure or amino acid sequence shared among different proteins. They are recognizable regions of protein structure that may (or may not) be defined by a unique chemical or biological function.

A sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. A protein sequence motif is an amino-acid sequence pattern found in similar proteins; change of a motif changes the corresponding biological function.

The proteome is larger than the genome, especially in eukaryotes, in the sense that there are more proteins than genes. This is due to alternative splicing of genes and post-translational modifications like glycosylation or phosphorylation.

The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. … Single-cell transcriptomics allows tracking of transcript changes over time within individual cells.

The general goal of proteomics is to monitor the properties of the entire complement of proteins from a given cell or organism, and to determine how these properties change in response to various physiological states, such as signaling ligands, cell cycle, and disease.

Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula, C400H620N100O120P1S1.

The first step in protein synthesis is called transcription. Transcription is the process wherein DNA is used to create messenger RNA, or mRNA. The mRNA is produced using DNA’s code, which is contained within the cell’s nucleus.

The main difference between proteomics and transcriptomics is that the proteomics is the study of the entire set of proteins produced by a particular organism whereas the transcriptomics is the study of the entire set of mRNA synthesized by a particular organism.

Folded proteins are held together by various molecular interactions. During translation, each protein is synthesized as a linear chain of amino acids or a random coil which does not have a stable 3D structure. The amino acids in the chain eventually interact with each other to form a well-defined, folded protein.

Proteome Mapping is a technique in which the proteome is analysed by LCMS: a combination of chromatography separation and mass spectrometry. Pure protein sample is digested and run through an extended 1- or 2-D LC gradient, and the eluent injected into a LCMS instrument.

The mass spectrometry proteomics experiments currently come in two general flavors: In one approach, proteins from a cell extract are first separated by two-dimensional (2D) gel electrophoresis. Then, proteins on the gel are identified by measuring their masses with MALDI-TOF mass spectrometry.

A profile card is a card that contains saved profile keys and profile values. They allow you to assign profile values consistently across all items on your website.

Pattern card is a term used in the industry to describe a record of the pattern style. It will will contain a list of all of the pieces in the pattern set.

In Bioinformatics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has been proven or assumed to have a biological significance. … The problem is to discover the motifs, i.e. what is the order of letters the particular motif is comprised of.

Use SQL Server Profiler Microsoft SQL Server Profiler is a graphical user interface to SQL Trace for monitoring an instance of the Database Engine or Analysis Services. You can capture and save data about each event to a file or table to analyze later.

Think of it this way: SQL profiles give information to the optimizer to help select the best plan but don’t force the optimizer to select any specific plan. SQL plan baselines limit the optimizer plan selection to a set of accepted plans.

A default profile can be created – a default already exists within Oracle named DEFAULT – it is applied to any user not assigned another profile. Assigning a new profile to a user account supersedes any earlier profile. Profiles cannot be assigned to roles or other profiles.

Available Genome-Wide Searches. Genome BLAST services are available at NCBI for a variety of organisms including human, mouse, rat, fruit fly, and many others in a growing list. At a minimum, MegaBLAST and “blastn” searches against the complete genome are supported.

The Expect threshold (“E”) is a BLAST parameter that reflects the number of matches expected to be found by chance. If the statistical significance of a match is greater than the Expect threshold, the match will not be reported. The E threshold default is set to 10.

RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database of profiles. This is the opposite of PSI-BLAST that searches a profile against a database of sequences, hence the ‘Reverse’. … RPS-BLAST was coded by Sergei Shavirin with some help from Tom Madden.

Protein structure databases are critical for many efforts in computational biology such as structure based drug design, both in developing the computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein.

This protein sequence database provides a high level of annotations (such as a description of the function of a protein, its domain structure, post‐translational modifications and variants) and a high level of cross‐linked integration with about 60 external databases.

Of these, the most important are the equivalent DNA databases European Molecular Biology Laboratory (EMBL), GenBank and DNA Databank of Japan (DDBJ), and the protein databases Swiss-Prot and TrEMBL.