Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

Abstract

The present review attempts to cover a number of methods that have appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this review to conventional two-dimensional (2-D) map analysis which couples orthogonally a charge-based step (isoelectric focusing) to a size-based separation step (sodium dodecyl sulfateelectrophoresis). The first and oldest method applied to 2-D map data reduction is based on statistical analysis performed on sets of gels via powerful software packages, such as Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately running a number of replicas for control and treated samples. The two sets of data are then merged and compared via a number of software packages which we describe. In addition to commerciallyavailable systems, a number of home made approaches for 2-D map comparison have been recently described and are also reviewed. They are based on fuzzyfication of the digitized 2-D gel image coupled to linear discriminant analysis, three-way principal component analysis or a combination of principal component analysis and soft-independent modeling of class analogy. These statistical tools appear to perform well in differential proteomic studies.

Development of an integrated approach for evaluation of 2‐D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2‐D gel/MALDI workflow

“…The protein spots were visualized by colloidal Coomassie blue (CCB) staining using a NOVEX CCB staining kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer protocols. The CCB-stained gels were scanned using a Typhoon 9400 laser scanner (GE Healthcare) and raw image files were analyzed by Progenesis software version 2005 (Nonlinear Dynamics, Newcastle-upon-Tyne, UK) [28,29]. The average normalized volumes for each spot (% of total spot volume) from each sample group containing triplicate gel images were compared, and the spots with at least a two-fold differential expression between WT and Or samples were subjected to subsequent protein identification analysis.…”

Proteomics of marine bacteria

“…Low and high salt concentrations 2-D PAGE and MALDI-MS [52] Heat shock 2-D DIGE and [ 35 S]methionine pulse-labelling combined with 2-D PAGE and MALDI-MS [54] Biofilm-specific proteins 2-D PAGE and MALDI-MS/MS or nano-LC-ESI-MS [79] Aerobic and anaerobic conditions 2-D PAGE and MALDI-MS [90] Cell isolation of symbiotic cells Cell density centrifugation to separate bacterial cell populations [14,15] Cell disruption of mixed bacterial assemblages Sonication with different lysis buffers [122] Image analysis Quantitative analysis of 2-D maps [37] Gel-image warping and quantitative analysis [38] 2 Marine genome sequencing projects…”

“…In recent years the computer-based evaluation of 2-D gels has significantly increased (as reviewed in ref. [37,38]). Specific software tools facilitate a precise quantitative assessment of proteome patterns, offering the additional opportunity to numeralize and relativize changes in protein spot volumes.…”

The pitfalls of proteomics experiments without the correct use of bioinformatics tools

“…Over the past decade, an important number of commercial softwares involving more powerful algorithms and statistical tools than the previous generations of such programs were designed to help researchers deal with the sheer quantity of data produced. Table 1 summarises the commercial softwares presently available and homemade systems for proteomics researchers [41][42][43][44][45][46]. A series of articles published elsewhere [8,[46][47][48][49][50][51] compare and contrast the softwares developed for 2-DE analyses.…”