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Training & Protocols


Many of the terms found in his glossary are specific to PNNL's Proteomics Facility.

Other glossaries are found on the Links page.



The experimentally determined amount or intensity of a peak in a given mass spectrum.
Accurate Mass and Time Tag (AMT)
Unique mass and time tag whose nucleotide coding sequence appears in exactly one Open Reading Frame (ORF) in an organism's genome.
Analysis Job
A single post-acquisition analysis step performed on raw mass spectral data, which can take the form of total ion chromatogram (TIC) generation, peptide identification of ion trap MS/MS data, or isotopic peak deconvolution for FTICR-MS data.


Best Score [Mass and time Tag List]
The highest SEQUEST XCorr score observed for any peptide constituent of a given mass and time tag, regardless of Mass and Time Tag Subset. Biomass Source The initial source of biological material for a given protein sample. This can be in the form of a Cell Culture for prokaryotic species, a tissue or other source. A biomass source belongs to a particular campaign, but may be associated with several experiments.
Biomaterial Preparation
The process of preparing a Biomass Source for further sample processing. This includes the introduction of changes in growth conditions, environmental stressors, and/or metabolic labeling. This step may be performed either by the researcher prior to sample submission, or by researchers at the Proteomics Facility. The Biomaterial Preparation process is tracked by the Cell Culture tracking entity in PRISM.


An association of related experiments that represent a major line of investigation.
Candidate Peptide
A peptide identified by SEQUEST from preliminary ion trap MS/MS data that is awaiting promotion to become an Accurate Mass and Time (AMT) Tag
Cell Culture
The initial source of biological material for a given prokaryotic protein sample. Also used generically by the Data Management System (DMS) to refer to a Biomass Source. A cell culture belongs to a particular campaign, but may be associated with several experiments.
A yet-to-be-implemented value representing the degree of certainty in the identification of a given mass and time tag
Confirmed Mass and Time Tag
Mass and time tag having one or more associated FTICR peak results.


Data Management System (DMS)
The PRISM subsystem that is responsible for capturing and storing raw mass spectral data, as well as maintaining tracking metadata regarding Campaigns, Cell Cultures, Experiments, Datasets, and Analysis Jobs
Describes everything related to a single mass spectrometer run, including details of the separation method and the names of the associated raw MS data files. A dataset belongs to a single experiment, but an experiment may give rise to multiple datasets.
Dataset Folder [DMS]
Folders which contain all the files resulting from a single MS run on a given instrument, including any subsequent intermediate results files generated from the raw spectra by Analysis Jobs. Dataset folders are created inside an Instrument Folder.
Dataset Rating [DMS]
Researcher-assigned value that specifies whether a dataset should be considered for subsequent processing or inclusion in Mass and Time Tag Databases. Currently limited to values of 'Interest', 'No Interest', or 'Unknown'.
Dataset State
Describes where in the capture process a given Dataset presently is. Possible values are 'New', 'In Progress', 'Complete', or 'Capture Failed'.
Development [Mass and Time Tag Database State]
A Mass and Time Tag Database that is in the process of being created or tested. Automatic updates are not performed on these databases, so their data should not be presumed valid or complete for general research purposes.


Describes the protocols and handling used to prepare an enzymatically digested protein sample for analysis by mass spectrometry. An experiment belongs to a single campaign, but may be associated with several biomass sources to allow for metabolic labeling experiments.
Expression Ratio
A representation of the difference in abundance for a given protein or peptide produced under different growth conditions or environmental stresses.


Final Data Processing
The process by which a suitable group of peptides resulting from the Intermediate Data Processing step are filtered and selected according to a given set of criteria established for each Mass and Time Tag Database. This builds a set of Putative Mass and Time (PMT) Tags from the set of peptide identifications which can then be correlated with FTICR-MS analyses to yield Accurate Mass and Time (AMT) Tags. Each of the many mass and time tag databases in PRISM is limited to a single organism and campaign, but can have its own unique set of filtering criteria.
Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS)
An ultra-high resolution mass spectrometer which uses the measurement of the motions of ions in a magnetic field to deliver very high mass measurement accuracy.
Frozen [Mass and Time Tag Database State]
A Mass and Time Tag Database whose development has been suspended, usually retained as a reference to provide a "snapshot" of the data at a given moment in time. Automatic updates are no longer performed.


High Score [Mass and Time Tag List]
The highest SEQUEST XCorr score observed for any peptide constituent of a mass tag in a given Mass and Time Tag Subset.


A PC-based data processing software suite that provides a wide range of functionality to support research. These capabilities include broad aspects of waveform generation, data acquisition and data analysis.
Instrument Folder [DMS]
A DMS data storage entity which contains all of the data and related files produced from a specific mass spectrometer.
Intermediate Data Processing
The process by which raw mass spectral data are analyzed by various programs to produce the intermediate results that subsequently feed into the Mass and Time Tag System. Generally, ion trap MS/MS data are processed by SEQUEST to provide peptide identifications, and FTICR spectra are processed by ICR-2LS to provide deconvoluted lists of peaks. These processes are controlled and tracked by the Analysis Job tracking entity.
Isotope Coded Infinity Tag (ICAT)
One of the many stable isotope labeling methods that provide the ability to both identify and quantify a broad range of proteins in a high-throughput mode. Using ICAT reagents, researchers can compare the expression levels of proteins from two samples, such as from normal and diseased cells. ICAT reagents comprise a protein reactive group, an affinity tag (biotin), and an isotopically labeled linker.


AMT tags that are used to assist mass calibration which are manually assigned from highly confident identifications resulting from FTICR-MS/MS analyses.


A peptide identification search engine which uses a probability-based scoring algorithm to analyze mass spectrometry data against primary sequence databases. Similar to SEQUEST.
Mass Spectrometer
A scientific instrument used for measuring the mass-to-charge ratio (m/z) of ions. Mass spectrometers generally couple three devices: an ionization device, a mass analyzer, and a detector. The most common ionization techniques used in biological MS are electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). Once a sample has been ionized, it must be separated on the basis of mass. The most commonly used mass analyzers for protein biochemistry applications are FTICR-MS, time-of-flight (TOF), triple-quadrupole, and ion trap instruments.
Mass Spectrometry Process
This process injects an aliquot from a sample into a mass spectrometer through a high-pressure capillary liquid chromatography column. The result is a sequence of mass spectra taken at intervals. The output data and the description of the spectrometer run are tracked by the Dataset tracking entity in PRISM.
Mass Spectrometric Analysis
A method for determining the Mass-to-Charge Ratio (m/z) of an ion.
Mass and Time Tag Database
A mass and time tag database draws its input information from the peptide database and creates mass and time tags and matches peak results to them. Each mass and time tag database is limited to a single organism and campaign, but can have its own unique set of filtering criteria. It associates with an ORF database in order to correlate rich genome information to each of the mass tags.
Mass and Time Tag Subset
Researchers are interested in comparing proteins observed under different conditions of growth and stress in the organism. The mass and time tag database provides a facility for selecting subsets of mass and time tags based on criteria that can be specified at many points in the reference chain. For example, the researcher may define a mass and time tag subset for each of the different stressors applied to an organism in a campaign. Many of the MTS display pages are designed to filter on these mass and time tag subsets, and the researcher can observe the effects that the stressors had on the mass and time tags that were observed (and by inference, the effects incurred by their parent proteins).
Mass and Time Tag System (MTS)
The PRISM system responsible for identifying PMT Tags from SEQUEST results, as well as confirming and validating AMT Tags using ICR-2LS peak results.
Mass-to-Charge Ratio (m/z)
Denotes the dimensionless quantity formed by dividing the mass of an ion by its charge.


Normalized Elution Time (NET)
NETs are generated from a simple curve-fitting algorithm that normalizes the total ion current (TIC) profile against a reference version.


Open Reading Frame (ORF)
Corresponds to a region of nucleotide sequence that may potentially be translated into a protein. This region usually begins with a "start" codon (nucleotide sequence 'ATG') and terminates with one of 3 "stop" codons. An ORF is not usually considered equivalent to a gene or locus until there has been shown to be a phenotype associated with a mutation in the ORF, and/ or an mRNA transcript or a gene product generated from the ORFs DNA has been detected.


Parameter File
Specifies analysis software parameters.
The deconvoluted, mass-domain of an isotopic distribution resulting from FTICR mass spectrometry analysis of an ion.
Potential Mass and Time Tag (PMT Tag)
Mass and time tag that has no associated peak results.
Pre-Production Database
Production state in which mass and time tag database is active. Updates are automatic, but final QC on data is pending.
A job parameter that specifies the order in which an Analysis Job should be handled. Lower values equate to higher priorities.
Production Database
Production state in which Mass and Time Tag Database is active. Updates are automatic and final QC on data is complete.
Proteomics Research Information and Management System (PRISM)
Collects data files from multiple mass spectrometers and manages the storage and tracking of these data files as well as automates their processing into intermediate results and final products. Also collects and maintains information about the biological samples used in research experiments and the laboratory protocols and procedures used to prepare them. Finally, the system allows users to locate and examine the data that it contains, and allows other information systems to access appropriate portions of it. The final products of the system are compilations of peptides observed in the biological samples for a particular organism under specified sets of conditions chosen by the researchers in their experiments. Researchers query these compilations to determine what proteins an organism creates under different conditions of growth and stress in order to better understand the how cellular biological mechanisms work.


Quadrupole Ion Trap
A relatively low-cost, versatile Mass Spectrometer which determines Mass-to-Charge Ratio (m/z) by manipulating ions within a hyperbolic-geometry trapping cell. Sample Preparation The process by which a Biomass Source is prepared for Mass Spectromic Analysis. This can include processes such as cell lysis, cell component fractionation, proteolytic digestion of protein contents, and final sample cleanup. The output from this process is referred to as a Sample. Each sample generally is sufficient to provide several aliquots for injection and separation on the LC-MS system. Samples are tracked by PRISM using the Experiment entity.


Software package that performs peptide identification by correlating experimental MS/MS spectra with theoretical mass distributions generated from an organism's protein sequence database.
Settings File
This optional file contains instructions that the analysis manager will interpret. It is used to specify options for the analysis tool program are not implemented in the parameter file - the analysis manager imposes them as command line arguments when it launches the analysis tool program. However, there are also cases where instructions in the settings file are intended only for the analysis manager.


Tandem Mass Spectrometry (MS/MS)
A tandem MS, or MS/MS, instrument performs two major steps during the acquisition of a spectrum. After a complete mass spectrum is taken to determine all of the ions present, a selection of the most abundant ions are sequentially isolated and subsequently fragmented by colliding them with neutral gas molecules in the spectrometer. The resulting fragments are then recorded as a separate mass spectrum. This second stage of mass analysis allows information about the structure of the fragmented ions to be collected and analyzed.
Time-Of-Flight Mass (TOF) Spectrometer
A type of mass spectrometer that relies upon the principle that ions given the same initial amount of translational energy, but having differing Mass-to-Charge Ratios (m/z) require different amounts of time to travel a certain distance along a field-free flight regions within the mass spectrometer. By counting the ions arriving at the detector at any given time, a mass spectrum can be built up from the arrival distributions.
Tracking Entity
DMS uses various entities to keep track of both data and results files, as well as metadata to coordinate their handling and maintain contextual information regarding their origins. These metadata can include such things as background information on the experiment, growth and stress conditions for the initial biomass source from which the protein sample resulted, sample digestion and processing conditions, as well as experimental factors such as chromatographic separation conditions or peptide identification parameters. These entities are arranged in a hierarchical fashion that represents the actual structure of our experimental process.


The peptide identification cross-correlation score reported by SEQUEST. Represents the degree of similarity between the experimental mass spectrum and a theoretical mass distribution generated for a given ORF.