Data Analysis

2D-Gel Matching

Matched Hep-G2 database of the WITA-Proteomics AG toxicity marker study1.
The database consists of 52 gels. The 53th gel (top right corner, brighter background) is the synthetic gel created after evaluation of all spot pair files. During spot pairing each gel had been reference gel once.This medium sized database attributes a total of 185988 spots to 6800 spot groups.
(Courtesy of Eurogentec SA, Seraing, Belgium)

High gel to gel reproducibility, a staining method capable of displaying a high linear dynamic range, the 2D-gel evaluation software chosen, rigorous spot editing following software supported spot recognition, a set of reliable well distributed landmarks and operator experience are the main factors that determine the matching quality of a 2D-gel database. While the influence of the experimental parameters is quite obvious, the contribution of different 2D-gel evaluation software packages is much less.

Significant differences exist throughout commercially available software concerning the quality of spot detection and matching as well as the ease of manual editing at the different stages of the process. Additionally, differences exist towards the approach of matching: While some software supports to pair each gel of a match set just against a single "reference gel", other software packages follow the concept of the "synthetic gel". The synthetic gel is thereby only constructed after spot pairs have been determined for each possible pair of gels of a match set. This means that each gel of a match set had been used as "reference gel" once during the matching process.
Although the latter concept requires more CPU-time to process in the first place, it on the other hand significantly improves the coverage of spot groups within the software assembled 2D-gel database. If, on the other hand, only a single reference gel is selected for a match set, the problem arises that spots which belong to spot groups that are not represented by a spot in the reference gel do not form groups within the software assembled 2D-gel database. The initial advantage of the "single reference gel approach" in CPU-processing time is readily lost by the succeeding manual editing effort or has to be paid for by the loss of the most interesting spots, i.e. protein forms just induced or completely inhibited by treatment.

The latest developments in 2D-gel matching constitute the "all to all"-matching concept of Ludesi AB, Lund (Sweden). The implementation of this 2D-gel analyzer solution on fast vector machines avoids the pitfalls of reference gel based gel matching and offers high analysis speed for larger match sets.

1Thome-Kromer B, Bonk I, Klatt M, Nebrich G, Taufmann M, Bryant S, Wacker U and Köpke A.