PROTEOMER: A workflow‐optimized laboratory information management system for 2‐D electrophoresis‐centered proteomics

Abstract

In recent years proteomics became increasingly important to functional genomics. Although a large amount of data is generated by high throughput large-scale techniques, a connection of these mostly heterogeneous data from different analytical platforms and of different experiments is limited. Data mining procedures and algorithms are often insufficient to extract meaningful results from large datasets and therefore limit the exploitation of the generated biological information. In our proteomic core facility, which almost exclusively focuses on 2-DE/MS-based proteomics, we developed a proteomic database custom tailored to our needs aiming at connecting MS protein identification information to 2-DE derived protein expression profiles. The tools developed should not only enable an automatic evaluation of single experiments, but also link multiple 2-DE experiments with MS-data on different levels and thereby helping to create a comprehensive network of our proteomics data. Therefore the key feature of our "PROTEOMER" database is its high cross-referencing capacity, enabling integration of a wide range of experimental data. To illustrate the workflow and utility of the system, two practical examples are provided to demonstrate that proper data cross-referencing can transform information into biological knowledge.

Protocol: a fast, comprehensive and reproducible one-step extraction method for the rapid preparation of polar and semi-polar metabolites, lipids, proteins, starch and cell wall polymers from a single sample

“…phosphorylated or glycosylated proteins or peptides are readily available [74, 75]. Not to mention, that the obtained protein extract can be efficiently used for gel-based separation in combination with mass spectrometry-based proteomic analysis, 2D-gel-based proteomics, phosphoproteomics or simply western blotting [73, 76]. …”

Kainate Promotes Alterations in Neuronal RNA Splicing Machinery

“…Peptides were analyzed by an ESI−MS/MS on a LCQ Deca XP ion trap instrument (Thermo Finnigan, Waltham, MA). Alternatively, a Reflex 4 MALDI-TOF mass spectrometer (Bruker Daltonics, Bremen Germany) was used for identification, as described previously. ,,− Mass spectra were analyzed using our in-house MASCOT software package (version 2.1) automatically searching NCBI databases (SwissProt, version 51.8).…”

The use of chemometrics to analyse protein patterns from gel electrophoresis

“…Based on increasing computer capacity and the availability of information in databases there is now a growing field of data analysis techniques focusing on utilizing information from databases and literature to reveal interactions and regulatory network. The outputs usually consist of graphic displays of networks grounded on principles derived from graph theory [1,79,127,157,[223][224][225][226][227][228][229][230][231][232][233][234][235]. The network methods partition the interaction network into functional modules, and represent interaction networks by complex graphs in which nodes correspond to proteins and edges corresponds to the interactions.…”