Comparison of PDQuest and Progenesis software packages in the analysis of two‐dimensional electrophoresis gels

Rosengren, Arsi T.; Salmi, Jussi; Aittokallio, Tero; Westerholm, Jan; Lahesmaa, Riitta; Nyman, Tuula A.; Nevalainen, Olli

doi:10.1002/pmic.200300544

Cited by 80 publications

(51 citation statements)

References 26 publications

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“…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.…”

Section: -De and Image Analysismentioning

confidence: 99%

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

Yang¹,

Thannhauser²,

Li³

et al. 2007

Electrophoresis

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With 2-D gel mapping, it is often observed that essentially identical proteins migrate to different positions in the gel, while some seemingly well-resolved protein spots consist of multiple proteins. These observations can undermine the validity of gel-based comparative proteomic studies. Through a comparison of protein identifications using direct MALDI-TOF/ TOF and LC-ESI-MS/MS analyses of 2-D gel separated proteins from cauliflower florets, we have developed an integrated approach to improve the accuracy and reliability of comparative 2-D electrophoresis. From 46 spots of interest, we identified 51 proteins by MALDI-TOF/TOF analysis and 108 proteins by LC-ESI-MS/MS. The results indicate that 75% of the analyzed spots contained multiple proteins. A comparison of hit rank for protein identifications showed that 37 out of 43 spots identified by MALDI matched the top-ranked hit from the ESI-MS/MS. By using the exponentially modified protein abundance index (emPAI) to determine the abundance of the individual component proteins for the spots containing multiple proteins, we found that the top-hit proteins from 40 out of 43 spots identified by MALDI matched the most abundant proteins determined by LC-MS/MS. Furthermore, our 2-D-GeLC-MS/MS results show that the top-hit proteins in 44 identified spots contributed on average 81% of the spots' staining intensity. This is the first quantitative measurement of the average rate of false assignment for direct MALDI analysis of 2-D gel spots using a new integrated workflow (2-D gel imaging, "2-D GeLC-MS/MS", and emPAI analysis). Here, the new approach is proposed as an alternative to traditional gel-based quantitative proteomics studies.

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Section: -De and Image Analysismentioning

confidence: 99%

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

Yang¹,

Thannhauser²,

Li³

et al. 2007

Electrophoresis

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“…A number of software packages have appeared in the last decade and are listed in Table 1. A few papers have been published comparing some of these packages: PDQuest and Progenesis [1]; Z3 and Melanie 3.0 [2]. Other reports assess just a single product, e.g.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2005

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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.

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“…A variety of commercial 2-DE analysis software packages are available to perform such tasks in a highly reproducible and automated manner, e.g. ImageMaster (GE Healthcare), PDQuest (BioRad) and Progenesis (Nonlinear Dynamics) (Garrels, 1989;Appel et al, 1991;Rosengren et al, 2003;Medberry et al, 2005).…”

Section: Historical Overview Of 2-dementioning

confidence: 99%

Two-dimensional gel electrophoresis in bacterial proteomics

et al. 2012

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Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.

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Comparison of PDQuest and Progenesis software packages in the analysis of two‐dimensional electrophoresis gels

Cited by 80 publications

References 26 publications

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

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

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

Two-dimensional gel electrophoresis in bacterial proteomics

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