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The First 2D Gel Analysis Software Exclusively for Host Cell Protein (HCP) Coverage Analysis

HCP coverage software
  • Bioassay Development:

Host cell protein (HCP) and anti-HCP antibody characterization via 2D gels and Western blots.

  • Bioprocess Improvement:

Assess the purification of biologic production through comparison of multiple 2D gels.

  • Analytical Development:

Developing process-specific immunoassays for use in host cell protein (HCP) analysis of new biologics and biosimilars.

HCP coverage software

Used By Top Biopharmaceutical, Biotechnology, Chemical Companies, Leading Research Organisations & Top Universities Around The World For Analytical Development

Easy to use, fast, objective analysis developed for:

  • 2D gel and 2D Western blot,
  • 2D Differential in Blot Electrophoresis (2D-DIBE),
  • 2D Fluorescence Difference Gel Electrophoresis (2D-DIGE), using any stain including CyDyes.

“SpotMap played an integral role in our comparison of proteomes of different cell lines during the process of choosing a proper antigen for antibody development. […] With this software, my team was able to make a more informed choice on the best candidate to use for our purposes.”

Virginia Liu-Compton

Research Associate 2, ImmunoGen Inc.

SpotMap Example Analysis Report using challenging 2D Gel and Western blot images

Reproducible results in less than 1 hour

An example report to illustrate how quickly you can analyse challenging 2D gels and Western blots to calculate host cell protein  (HCP) percentage coverage.

Latest reports and evidence for inter-user inter-lab reproducibility, accurate analysis techniques, fast host cell protein coverage results and more.

Helps To Support 21 CFR Part 11 Compliance

As the biopharmaceutical sector continues to grow, it faces an increased regulatory burden from global drug administrations. SpotMap offers a novel solution to host cell protein (HCP) coverage analysis and is designed with an extra level of regulatory consideration.

You can now obtain complete and accurate records of your analysis helping to adhere to the new regulatory guidance and quality consideration standards of the FD&C Act in regards to process-related impurities.

Exclusive Features Include:
  • Secure data reporting
  • Customisable reports and additional data inputs
  • Full audit trail of users, actions and time records

“Once we had the images put through the SpotMap software it corresponded to areas that personally I would have never matched (which ended up being the correct areas). The best part is I can depend on the results.”

Craig Pattinson

Research Technician, Proteomics, Aberdeen University, The Institute Of Medical Sciences

Host Cell Protein Analysis 21CFR Report
PDF Analysis

Complete Host Cell Protein Coverage Analysis Report With Audit Trail

Analysis report and audit trail generated under an hour using challenging gels.

Reproducible Host Cell Protein Coverage Results

Remove subjectivity from your editing process – Complex sample preparation and running procedures cause distortions such as faint spots, overlapping spots, saturated spots and streaks making analysis of 2D gels and Western blots difficult.

Automatic analysis tools remove the need for subjective decisions in image analysis, and visuals of spot intensity, volume, peak height and colour overlay tools give you confidence when determining the authenticity of a spot.

Tools designed for 2D and Western blot analysis include:

  • Filters
  • Automatic spot detection
  • Automatic alignment
  • 3D and colour visualisation

Figure 1. (right) shows an increased visual of low abundance spots found on a gel image using the colour overlay tools.

“One feature that I found to be especially useful was the 3D view which allowed for a better visual of spot intensity when determining spots. The table of identified spot for each image also made it easy to identify which spots are unique or common to the different images.”

Virginia Liu-Compton

Research Associate 2, ImmunoGen Inc.

With SpotMap, you can be more confident that the spots you see on your images reflect the actual proteins which the antibody recognised.

Inter- user Variation Poster

Reproducible Coverage Results Between Users & Labs (less than 10% variation) 

Four analysts from two locations with a range of experience analysed two data sets and the percentage coverage results were compared. The coefficient of variation for each analysis was within 10%.

Simple To Use & Fast Adoption

Become an expert user in a fraction of the time-  SpotMap puts you back in control of your analysis with a single flexible user interface optimised for 2D gel and Western blot comparison.

Studies show users can complete reproducible analyses in less than 1 hour.

Single, fast analysis tool- Address your common challenges such as gel distortion, positional variation, image quality and spot detection at any point during your experiment. Other analysis software restricts your experiment with predetermined workflows or slow work around techniques that let some of your data slip away.

SpotMap is developed for the specific purpose of anti-HCP antibody characterisation and relative coverage calculation. Supporting techniques including:

  • 2D-Single Stain
  • 2D-DIGE
  • 2D-DIBE
  • AAE

“I have found the software very easy to use and has been exactly what I needed to compare western blots and pick the spots from my gel”

Rebecca Oettle

Phd Student, University Of Cambridge

Inter- user Variation Poster

Minimal variation between users (±2%)

This report assesses SpotMap across three data sets of varying difficulty, by three users of varying expertise to obtain the host cell protein coverage result. In conclusion, percentage coverage is within a range of 2% using an easy data set and percentage coverage is within a range of 10% using a challenging data set.

Minimal User Intervention

Improved spot detection – Low abundance spots, distorted spots, overlapping spots, spots suffering from noise, saturated spots, streaking and the presence of non-spot features are common issues faced in 2D analysis and consequently make spot detection difficult and decrease the objectivity of the analysis.

SpotMap has highly improved imaging techniques for intuitive automatic spot detection reducing the need for manual detection.

“We have had real difficulty matching reactions on blots to the corresponding areas on the gels. With our previous technology it genuinely wasn’t possible so adding the SpotMap software to our facility has helped greatly.”

Craig Pattinson

Research Technician, Proteomics,, Aberdeen University, The Institute Of Medical Sciences

Poster: Removal of Positional Variation in SpotMap
Application Note

Accurate methods to remove positional variation in 2D gel and WB comparison

The use of additional images to be used as the alignment targets can simplify the alignment process in some cases. Whichever approach is used it should be similar or the same each time a new analysis is used for reproducible results.

Ready to try SpotMap for yourself?

1. Demonstration

Our application experts can answer any questions you have on the software or advise you on your latest analysis. You will get access to the following:

  • Best practices for achieving reproducible results.
  • Tips for aligning challenging gels and blots.
  • Which tools to use for challenging images for e.g. faint spots.
  • How to quickly produce and export reports and audit trails
2. Free Trial

Don’t take our word for it. You will now be ready to test the performance of SpotMap yourself using your own images for free.

During the trial you will have access to our support and analytical team for advice and to answer any technical questions you may have. We aim to respond to any queries within 24 hours Monday – Friday.



The software is going to be used in a cGMP lab. Is SpotMap suitable for the regulatory requirement including 21 CFR?

SpotMap now has new tools which help compliance with 21 CFR part 11 and is now the only software developed for immunoassay development, analytical development and bioprocess improvement that aims to support new regulatory requirements.

Can I compare different spot patterns found between my 2D gels and Western blots?


Alignment is a key feature within SpotMap. It removes positional variation between images to allow direct comparisons of spots present on different images to be made.

For further reading see our technical note which outlines and compares the use of two different alignment methods to remove positional variation and to calculate percentage coverage.

Our 1 minute online tutorials are designed to help you understand and learn the different visual cues in SpotMap and to understand the different software tools you can use to ensure you are confident using Alignment. Please go to the Alignment series to view.

What images formats can I use? Any recommendation on capturing my images?

SpotMap supports most industry-standard image file formats produced from laser scanners including JPG, PNG, GEL, MEL, TIFF (8-bit and 16-bit) and is compatible with most gel imaging/documentation systems.

We recommend scanning directly to grayscale as the imaging device will then do the conversion from colour in the most accurate and sensitive manner. We also recommend using the highest possible bit depth. For example, an 8-bit grayscale image file stores 256 shades of grey for each pixel, while a 16-bit image file has 65536 possible grayscale values for each pixel. For further technical details you can view our image capture guide or get in touch with us.

How much variability would you see between users?

Results obtained from our reports showed users were within a range of 10% of each other, when using the most challenging images. Users were in a range of 2% of each other when using easy data sets.

To illustrate, three data sets were used and analysed by three different users with varying range of experience which you can view here. Users analysed SpotMap to determine the relative coverage of the Western blot vs the 2D gel imageWe compared the percentage coverage results between each user.

Typically with 2D gels and 2D Western blots the biggest source of variation is the quality of the image used. The use of high quality images increase the objectivity and reliability in your results. Effects such as colour depth, saturation, streaking and presence of non-spot features reduce this objectivity. However using SpotMap you can overcome these challenges. Features unique to SpotMap enhance these visual distortions allowing a more informed and confident decision when necessary. In addition, tools such as interactive 3D, colour overlay mode and secondary image overlay easily overcome these challenges during your analysis by enhancing your images.

How long does an analysis usually take?

Multiple studies show that users can analyse their 2D gels and Western blots and produce objective results within one hour, even using challenging images. Examples illustrated in our evidence page.

Can I present my results and processes to external regulators?

The built-in report generator button exports your whole analysis in a clear, detailed PDF report and is the fastest way for third party regulators to view your results. In addition, you can export individual images and tables from your analysis if necessary.

The audit-trail exporter ensures accurate generation of a complete audit trail. These static electronic records identify who, what and when changes have been made in the project. This enhances transparency, prevents alteration which ensures the records exported are the original records and results.

How can I ensure my analysis is reproducible?

Factors that affect reproducibility in image analysis include:

  • Image cropping and resizing.
  • Number and location of alignment vectors.
  • Spot detection parameters used.
  • Definition of a spot.
  • The approach to editing the spot map, e.g. edit the detected spot pattern, or re-create a spot pattern in areas where individual spots are hard to identify.
  • Image Capture: When it comes to image capture then high resolution, 16-bit, grey-scale images, allow greater sensitivity and accuracy of results.


Automatic Alignment in SpotMap increases your reproducibility. In fact, Alignment is one of the most important features which actually removes positional variation between gel and blot images, providing easy comparison of spot patterns between images. Our video hints and tips series on Alignment answers common questions such as: how do I know that Alignment is correct & completed.

Automatic Spot detection is an intuitive automatic algorithm that identifies the location of spots in the project. This includes those hard to detect spots for example: low abundance spots.

Capture good images –16 bit images are recommended for analysis as these increase the intensity scale from 0-65535. You can find more advice and best practices required to generate digital images of a quality suitable for automated image analysis here. However SpotMap can analyse most image formats including 8 bit TIFF and lossy image formats.

Is your software compatible with my imager/gel documentation system?

SpotMap is compatible with most imaging/gel documentation systems and supports most industry-standard file formats, such as, JPG, PNG, GEL, MEL, TIFF (8-bit and 16-bit).

Thank you!

We’d like to thank all of our customers who gave us feedback on SpotMap. SpotMap is developed, maintained and improved and is the only software exclusively for host cell protein (HCP) coverage analysis developed in line with your feedback and needs.