Overcoming common challenges in 2D Proteomics
SameSpots
(previously Progenesis SameSpots) overcomes the common problems you
face when using 2D gel electrophoresis proteomics work to identify
differential protein expression analysis. These include a lack of
reproducibility in your results, hours of tedious spot editing and a
lack of confidence in the resulting statistical significance of protein
expression changes.
SameSpots
is simple to use and gives you fast, objective results for differential
expression of intact proteins using 2-DE gels.
- Simplicity. You are guided through each step of the workflow, new users can get up and running with minimal training.
- Speed. Typical analysis times of less than 5 minutes per gel with single-stain or 2-DE DIGE images.
- Objectivity. A consistent analysis approach that is proven to give reproducible results between different users.
- Statistical power. Image
alignment delivers 100% matching with no missing values in your data
for valid multivariate statistics.If
any quality issues are detected with your images prior to analysis, you
also have the opportunity within the system to make minor changes,
without changing the original image. This includes flipping images
horizontally and vertically, rotating images 90° clockwise or
anticlockwise, inverting the image and cropping the image.
Next-generation automated algorithms produce more accurate results, quicker
SameSpots uses a next-generation alignment-based approach to overcome positional variation introduced during the running and imaging of 2D gels which would typically prevent accurate comparison across multiple gels in large-scale proteomic experiments. These algorithms guarantee 100% matching of all spots with no missing values like those experienced in older pieces of 2D analysis software.The software then uses intelligent automation to automatically detect all of your protein spots and copy a single spot pattern across all images which ensures a high degree of analytical objectivity and reproducibility as well as eliminating laborious spot editing typical to other pieces of spot-matching software.
Due to the automated workflow, the software is simple-to-use and easy-to-train on – typically taking less than 2 hours for a new user to become fully trained and ready to produce accurate results. Our advanced automation also means that the analysis of a full dataset of images (usually up to 24 images) typically takes less than an hour.
Built-in Multivariate Statistical Analysis and Reporting Tools
Samespots is adaptable to your original experimental design, meaning you can perform full image and statistical analysis of your 2D proteomic studies within the same piece of software. This produces a comprehensive report that highlights to users when significant changes in protein expression are observed.
Samespots
currently supports the following types of experimental design and
associated statistical analysis:
• Between-subject Design (one-way ANOVA)
Do samples from your subject
appear in only one condition (for example, only in a control group)?
Samples are grouped according to experimental condition (defined by the
user) and an ANOVA test is performed to identify any significant
changes in protein expression between those groups. The ANOVA
calculation assumes that the conditions are independent and therefore
gives a statistical test of whether the means of every single spot
within all conditions is equal.
• Within-subject Design (repeated measures ANOVA)
Have you taken samples from a
given subject under different conditions?
This specialist repeated ANOVA test allows the user to tell the
software what experimental condition the sample came from along with
the unique subject that the sample came from, ideal for longitudinal
experiments where every subject has been sampled at every time point.
• Two-way ANOVA Design
Do your samples from a given
subject appear in two different conditions?
The two-way ANOVA allows users to determine
whether the
effect of one of your independent variables (e.g. drug treatment A) on
your dependent variable (e.g. protein expression) is the same for all
values of your other independent variable (e.g. drug treatment B) and
vice versa. This enables large scale clinical proteomic work to be
performed between different drug treatment profiles and their effects
on biomarker expression (significant or not).
Our
software is regularly used in agricultural proteomics so the above
studies can also be applied to testing variables such as genetically
modified seeds, disease resistance, plant supplements etc.
Delivering confidence in your 2D gel electrophoresis image analysis
The software is easy to use, with our experienced team providing you with a guided walkthrough of the workflow so you can quickly get to grips with the 2D gel electrophoresis image analysis software.Once up and running, typical analysis takes just five minutes per gel with either single-stain or 2D DIGE images.
Quick tags can also be used: these are useful for quickly highlighting proteins that show significant changes in expression. Therefore, you can focus your attention on these ‘interesting’ spots for further analysis with mass spectrometry. You can also import protein identification from mass spectrometry, from databases such as MASCOT or your own custom-made databases, back into your 2-DE analysis and report alongside quantitative results.