Kinesis is a leading international supplier of chromatography, liquid handling, sample storage and medicinal chemistry consumables and equipment. The ability to work. Protein Identification Protocol. For general methods and basics on protein identification by mass spectrometry, please review the following articles. Manual Syringe; Instrumentation. View All Instrumentation; Servicing. Pipette Servicing; Instrument Servicing; Brands. Bio-Works; Brand; Dibafit (Diba) ES Industries.
Manual control. a human performs some or all of the process control tasks (sense, compare, or correct). It looks like your browser might be zoomed in or out.
LC- MS/MS data. Reviewed by Jürgen Hartler,1,2. Gerhard G Thallinger,1. Gernot Stocker,1. Alexander Sturn,1. Thomas R Burkard,1. Erik Körner,3. Robert Rader,1. Andreas Schmidt,4.
Thermo Scientific BioWorks Installation Guide v P Preface About This Guide Welcome to BioWorks. The BioWorks software performs analyses of mass spectrometry data.
Karl Mechtler,5 and Zlatko Trajanoski. Institute for Genomics and Bioinformatics and Christian- Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 1. Graz, Austria. 2Austrian Research Centers Gmb. H - ARC, e. Health Systems, Reininghausstrasse 1. Graz, Austria. 3FH Joanneum, Kapfenberg, Werk- VI- Sraße 4. Kapfenberg, Austria.
Christian Doppler Laboratory for Proteome Analysis, Dr. Bohr- Gasse 3, 1. Vienna, Austria. 5Research Institute of Molecular Pathology, Dr. Bohr- Gasse 7, 1. Vienna, Austria. Corresponding author. Received 2. 00. 7 Apr 1.
Accepted 2. 00. 7 Jun 1. Copyright © 2. 00. Hartler et al; licensee Bio. Med Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http: //creativecommons. This article has been cited by other articles in PMC. Abstract. Background.
The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches. Results. We have developed the MAss SPECTRometry Analysis System (MASPECTRAS), a platform for management and analysis of proteomics LC- MS/MS data. MASPECTRAS is based on the Proteome Experimental Data Repository (PEDRo) relational database schema and follows the guidelines of the Proteomics Standards Initiative (PSI). Analysis modules include: 1) import and parsing of the results from the search engines SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA; 2) peptide validation, 3) clustering of proteins based on Markov Clustering and multiple alignments; and 4) quantification using the Automated Statistical Analysis of Protein Abundance Ratios algorithm (ASAPRatio).
The system provides customizable data retrieval and visualization tools, as well as export to PRoteomics IDEntifications public repository (PRIDE). MASPECTRAS is freely available at http: //genome. Conclusion. Given the unique features and the flexibility due to the use of standard software technology, our platform represents significant advance and could be of great interest to the proteomics community. Background. The advancement of genomic technologies – including microarray, proteomic and metabolic approaches – have led to a rapid increase in the number, size and rate at which genomic datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches. In contrast to genome sequencing projects, there is a need to store much more complex ancillary data than would be necessary for genome sequences. Particularly the need to clearly describe an experiment and report the variables necessary for data analysis became a new challenge for the laboratories.
Furthermore, the vast quantity of data associated with a single experiment can become problematic at the point of publishing and disseminating results. Fortunately, the communities have recognized and tackled the problem through the development of standards for the capturing and sharing of experimental data. The microarray community arranged to define the critical information necessary to effectively analyze a microarray experiment and defined the Minimal Information About a Microarray Experiment (MIAME) standard [1]. Subsequently, MIAME was adopted by scientific journals as a prerequisite for publications and several software platforms supporting MIAME were developed [2,3]. The principles underlying MIAME have reasoned beyond the microarray community. The Proteomics Standards Initiative (PSI) [4] aims to define standards for data representation in proteomics analogues to that of MIAME and developed the Minimum Information About a Proteomics Experiment (MIAPE) standard [5]. An implementation independent approach for defining the data structure of a proteomics experiment, the Proteome Experimental Data Repository (PEDRo) [6] was developed, and a PSI compliant public repository was set up [7].
Hence, given the defined standards and available public repositories, computational systems can now be developed to support proteomics laboratories and enhance data dissemination. To meet the needs for high- throughput MS laboratories several tools and platforms covering various parts of the analytical pipeline were recently developed including the Trans Proteomics Pipeline [8], The Global Proteome Machine [9], VEMS [1.
CPAS [1. 2], CHOMPER [1. Pro. DB [1. 4], PROTEIOS [1. GAPP [1. 6], Peptide.
Atlas [1. 7], EPIR [1. STEM [1. 9], and TOPP [2.
However, to the best of our knowledge there is currently no academic or commercial data management platform supporting MIAPE and enabling PRoteomics IDEntifications database (PRIDE) export. Moreover, it became evident that several search engines should be used to validate proteomics results [2.
Hence, a system enabling comparison of the results generated by the different search engines would be of great benefit. Additionally, integration of algorithms for peptide validation, protein clustering and protein quantification into a single analytical pipeline would considerably facilitate analyses of the experimental data.
We have therefore developed the MAss SPECTRometry Analysis System (MASPECTRAS), a web- based platform for management and analysis of proteomics liquid chromatography tandem mass spectrometry (LC- MS/MS) data supporting MIAPE. MASPECTRAS was developed using state- of- the- art software technology and enables data import from five common search engines. Analytical modules are provided along with visualization tools and PRIDE export as well as a module for distributing intensive calculations to a computing cluster. Implementation. The application is based on a three- tier architecture, which is separated into presentation- , middle- , and database layer.
Each tier can run on an individual machine without affecting the other tiers. This makes every component easily exchangeable.
A relational database (My. SQL, Postgre. SQL or Oracle) forms the database layer.
MASPECTRAS follows and extends the PEDRo database schema [6] (see additional file 2) to suit the guidelines of PSI [4]. The business layer consists of a Java 2 Enterprise Edition (J2. EE) compliant application which is deployed to the open source application server JBoss [2. Access to the data is provided by a user- friendly web- interface using Java Servlets and Java Server Pages [2. Struts framework [2. Computational or disk space intensive tasks can be distributed to a separate server or to a computing cluster by using the in- house developed JCluster.
Service interface. This web service based programming interface uses the Simple Object Access Protocol (SOAP) [2. MASPECTRAS server. The tasks can be executed on dedicated computation nodes and therefore do not slow down the MASPECTRAS web interface. This remote process execution system is used as a backend for the protein grouping analysis, for the mass quantification and for the management of the sequence databases and their sequence retrieval during import. The current implementation of MASPECTRAS allows the comparison of search results from SEQUEST [2.
Mascot [2. 7], Spectrum Mill [2. X! Tandem [2. 9], and OMSSA [3. The following file formats are supported: SEQUEST: ZIP- compressed file of the *. SEQUEST. params files; Mascot: *.
Spectrum Mill: ZIP- compressed file of the results folder including all subfolders; X! Tandem: the generated *. OMSSA: the generated *.
Raw data: XCalibur raw format (*. XML [3. 1] and mz. Data [3. 2] format.
The data can be imported into MASPECTRAS database asynchronously in batch mode, without interfering with the analysis of already uploaded data. The spectrum viewer applet and the diagrams are implemented with the aid of JFree. Chart [3. 3] and Cewolf [3. The whole system is secured by a user management system which has the ability to manage the access rights for projects and offers data sharing and multiple user access roles in a multi- user environment [2]. Results. Analysis pipeline. MASPECTRAS extends the PEDRo relational database schema and follows the guidelines of the PSI. It accepts the native file formats from SEQUEST [2.
Mascot [2. 7], Spectrum Mill [2. X! Tandem [2. 9], and OMSSA [3. The core of MASPECTRAS is formed by the MASPECTRAS analysis platform (Figure 1). The platform encompasses modules for the import and parsing data generated by the above mentioned search engines, peptide validation, protein clustering, protein quantification, and a set of visualization tools for post- processing and verification of the data, as well as PRIDE export. Schematic overview of the analysis pipeline of MASPECTRAS.
Search results from SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA are imported and parsed. In the next steps peptides are validated using Peptide.
Prophet [3. 7] and the corresponding proteins.. Import and parsing data from search engines. There are several commercial and academic search engines for proteomics data. Based on known protein sequences stored in a database, these search engines perform in silico protein digestion to calculate theoretical spectra for the resulting peptides and compare them to the obtained ones. Based on the similarity of the two spectra, a probability score is assigned.
The results (score, peptide sequence, etc.) are stored in a single or in multiple files, and often only an identification string for the protein is stored whereas the original sequence is discarded. However, the search engines are storing different identification strings for the proteins (e. X! Tandem: gi|2. 31. GPB|; Spectrum Mill: 2. Moreover, several databases are not using common identifiers (e. National Center for Biotechnology Information non redundant (NCBI nr): gi|6.
Mass Spectrometry protein sequence Data.
Bioworks: Affinity Media Work.