Guide: PEAKS Bioinformatics Software
What is the PEAKS software?
PEAKS is the tandem mass spectrometry proteomics analysis advanced software designed to sequence peptides, classify and quantify proteins.
PEAKS is widely used to classify peptides (protein ID) by scanning the search database with aid of de novo peptides. PEAKS comes incorporated with PTM and mutations by automated peptide sequence tag-based scanning (SPIDER).
For each peptide, PEAKS presents a full list, confidence levels on the individual assignments of amino acids, easy monitoring, and other details for high-performance analysis.
The app is capable of analyzing search engine returns. Cross tests with other protein Identification search engines, such as Sequest, OMSSA, X!Tandem and Mascot.
What is in the PEAKS Package?
PEAKS is advanced software for the analysis of peptide mass spectrometry data. The PEAKS family consists of: PEAKS Studio, PEAKS Online, PEAKS Client, and PEAKS Viewer.
What is PEAKS Studio?
PEAKS Studio performs de novo sequence, protein identification, metadata identification (PEAKS), hand-held, hand sequencing and information processing, whether online or independently. PEAKS Studio is a fully functional proteomic work bank.
All supported mass spectrometric data formats and native ANZ files are read by PEAKS Studio. Every copy of PEAKS studio should be installed and used by one user on a single computer of up to 4 CPUs.
What is PEAKS Online?
PEAKS Online, the server version, means that a shared resource is put to use. It is fully parallel and can be used on any cluster or multi-powered machine. PEAKS Online returns sequences auto de novo and identify Mass spectrometry (MS)/MS spectral data in peptides/proteins.
The results are shown on a built-in web server in HyperText Markup Language ( HTML). After analysis, links to the results are e-mailed to the user. In your institution, everyone with a browser, an e-mail address and access to the cluster can then provide information and view results.
What is the PEAKS client?
PEAKS client is the newest addition to the PEAKS family, takes and packages the best of PEAKS Studio and PEAKS. On the Studio side, a high-performance batch workflow can be used and organized with several files. The online effect enables the user to simultaneously establish and process raw data on a cluster and work.
What is the PEAKS Viewer?
The data reading device reads all of the mass data spectrometry formats and native ANZ files provided by PEAKS. It is intended to distribute PEAKS data results. You can view, edit and store the data. The auto Novo or protein ID algorithms are not used in PEAKS Viewer. Unlimited distribution capabilities were supported by the PEAKS of Viewer license awards.
Functions of Products/ Capabilities
De Novo Sequencing
In de novo sequencing technique, peptide sequences originate as seen on a tandem mass scale, from the masses of their fragments. No protein sequence database is used for comparison when carrying out de novo sequencing.
- The PEAKS provides a modified precise algorithm for auto Novo.
- PEAKS establishes an allocation of confidence at the level of amino acid.
- PEAKS can identify and position post-translation changes in peptides in the Novo series.
- PEAKS is specially built for the handling and use of y-and-b ions or z-ion for versatility in fragmentation data from Quadruntole Time-Of-Flight Mass Spectrometer (QTO FM), TOF-TOF, Ion Trap and Fourier Transform MS Instrumente (FTMS).
Using de novo sequencing methods such as PEAKS to help scan the databases. Protein identification Sequence tags are used to speed up the scan, delete false positive matches, and identify peptides with unusual sequence variations or changes that prevent them from being otherwise detected.
- inChorus Meta Protein ID – With this feature, PEAKS Studio Not only performs de novo sequencing and identifies proteins, but compares its results with those of such MS/MS databases as Mascot (see G6G Abstract Number 20087), OMSSA, SEQUEST, X! Tandem and sequence tag search tool SPIDER. Furthermore, you can eliminate false positives and recover false negatives by comparing to de novo sequences — this is automatic, at-a-glance information from PEAKS inChorus.
- SPIDER, Software Protein Identifier, is a sequence tag-based search tool, which can be used to identify peptides that traditional tandem mass spectrometry ion search tools will miss. SPIDER can also be used to improve coverage on a protein that is already in a database, by seeking exact sequence matches and being plugged into a specialized database.
Post Translational Modifications (PTMs)
PEAKS offers a range of features expressly designed to aid in the detection of altered proteins. PEAKS Studio uses scanning technology for the detection of PTMs, as well as de novo series. PEAKS allows for the identification of changes:
- A library of ~30 common PTMs (e.g. carbamidomethylation, phosphorylation, oxidation).
- A user-defined system for the creation of custom PTMs.
- Specify the modification(s) of interest and PEAKS will consider this information when providing sequence candidates or identification of proteins from your tandem MS spectra.
- The PEAKS auto de novo algorithm derives sequences with PTMs. The PTMs have then removed and both partial and complete sequence matches (i.e. tags) are used to search the database to find protein candidates. The shortlist of proteins in the database is then searched for spectrum-sequence matches, looking for variations in mass to identify PTMs. When this search finds a match with a PTM, the algorithm evaluates the quality of the match and provides the result with a final score.
Loading and Preprocessing RAW data
RAW data loading, refining and preprocessing algorithms are provided by PEAKS. Load RAW data directly into PEAKS from most devices or use a standard data format. Use the following:
- Melt the same peptide scans — The MS instrument is several times able to use the same peptide as MS / MS. Fusion of these scans ensures improved data quality. To avoid the mixing of the incorrect scans, PEAKS uses retention time and precursor load (m / z) value.
- Recalculate correct precursor charge: RAW data sometimes contains incomplete or incorrect details about the charge. But by analyzing the survey scan (or in the case of ion-trap data, the SM / SM itself), PEAKS may carefully recalculate it)
- Remove MS/MS scans that are of poor quality – A large percentage of MS/MS scans contain only noise. Removing these will speed up processing time, and reduce the risk of random false positive assignments.
- 4) Preprocess within MS/MS scans by –
- Baseline deduction noise filtering;
Requirements for Program
- The Sun’s Java Runtime Environment (JRE) 1.4 (or JRE 1.5 for PEAKS Studio 4.0 or later) can be running PEAKs on any device.
- PEAKS installs a dedicated JRE on the computer to allow it to exists on our system along with another version of Java.
- The machine should also be fitted with: 1-2 GB of RAM, 1 GB of free disk space (more for mass data and results), an AMD or 2GHz CPU from Intel.
- The minimum RAM and 1 GHz CPU is set up.
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