Image analysis resources library

2D gel quality control with SpotCheck: application note and 19-lab reproducibility study

How SpotCheck in SameSpots measures 2D gel reproducibility against a gold standard: a within-lab application note and a 19-lab study in which 18 labs produced passing gels.

How to capture quantitative western blot and gel images

How to capture western blot and gel images you can quantify: 16-bit grayscale, the linear range and the two kinds of saturation, choosing the exposure, resolution, file formats and a 12-point checklist.

Total protein normalization for western blots

How total protein normalization works, how stain-free, Ponceau S and fluorescent total protein stains compare, how to capture a valid total protein image, and how to normalize to total lane volume in Phoretix 1D.

Upgrading from TotalLab Quant, TL120 or TL100 to Phoretix 1D

Which current TotalLab product replaced TotalLab Quant, TL120, TL100 and TotalLab 1D, what carries over from your old installation, and how to move your SOPs and methods sections across.

Phoretix 1D vs ImageJ: Western Blot Quantification Compared

ImageJ western blot quantification step by step, where the free tool gives different answers to different people, and how Phoretix 1D automates the same densitometry.

Western Blot Densitometry: How Band Quantification Works

What western blot densitometry measures, why saturation and the linear range matter, how background subtraction changes the result, the calculation from raw image to ratio to control, and how to report it in your methods.

Phoretix 1D vs Image Lab: Bio-Rad Imager Owners’ Guide

Western Blot & Gel Analysis Software Compared (2026 Guide)

BioNumerics and GelCompar II Alternative

Host Cell Protein Resource Hub: Methods, Limits and Software

One starting point for host cell protein analysis. How ELISA, 2D gel and LC-MS compare, where each method stops working, what regulators actually require, and which questions to settle before you choose a platform. Links to every guide in the series, and to SpotMap MS for LC-MS and SpotMap 2D for gel-based coverage.

What HCP Antibody Coverage Percentage Is Acceptable?

There is no regulatory threshold for HCP antibody coverage. This resource traces where the 70 percent figure came from, explains why 2D gel and LC-MS coverage percentages are not comparable, and sets out what to state alongside any coverage claim, with SpotMap 2D producing the 2D gel coverage number you can defend.

AAV Host Cell Protein Analysis: Why mAb Methods Fail

AAV and lentiviral vector processes break the assumptions mAb HCP methods rely on: no null cell line, a capsid as the product protein, helper and packaging proteins in the mix, and no agreed ppm basis. This resource sets out what to measure instead and what to ask of an LC-MS workflow before you adopt one for gene therapy products.

DIA vs DDA for HCP Analysis: Reproducibility Explained

DDA re-picks precursors on every injection, so low-abundance host cell proteins appear and vanish between runs. DIA fragments every window. This resource explains what that means for HCP reproducibility and ppm trending, and what to ask of your analysis software before you commit to either.

High-Risk Host Cell Proteins: The Named Offenders, What They Do, and How to Find Them

Around 35 named high-risk host cell proteins sorted into BioPhorum's four impact categories, each with its primary citation, evidence type and detection route. Use it to build your watch list, then let SpotMap MS flag these proteins automatically in every LC-MS run.

USP 1132.1 Methods A, B and C Are Really 5.1.1 to 5.1.3

USP 1132.1 does not call its HCP quantitation methods A, B and C; they are sections 5.1.1, 5.1.2 and 5.1.3. Here is what each one spikes, what it calibrates against, how to qualify it against ICH Q2(R2), and how SpotMap MS lines your LC-MS workflow up with the chapter.

HCP ELISA vs LC-MS: Why Your ppm Numbers Disagree

An HCP ELISA and an LC-MS assay measure different things, so their ppm values rarely agree on the same sample. This resource explains the five mechanisms behind the gap, walks through a reconciliation, and shows how SpotMap MS gives you an LC-MS number you can put beside the ELISA result in a filing.

How to Calculate HCP ppm From LC-MS Data (ng/mg)

HCP ppm is nanograms of host cell protein per milligram of product protein, and the denominator you choose can double the answer. This guide works the arithmetic through twice, shows why USP measured 52 to 104 ng/mg on a single sample, and explains how SpotMap MS reports ppm on a stated, defensible basis every run.

How Custom Image Analysis Software for the Lab Is Built

OEM Instrument Software: White-Label, Co-Branded and Licensed

EU Annex 11 vs 21 CFR Part 11: What Software Must Do for Both

Validating Custom Software: GAMP 5, CSA and What to Expect

How to Choose a Life Science Software Development Partner

Custom vs Off-the-Shelf Scientific Software: How to Decide

GMP Compliant Software: What It Means and How to Check for It

Isoelectric Focusing and IPG Strips Explained: The 2D Gel First Dimension

Normalization in 2D Gel and 2D-DIGE Analysis: Methods Compared

2D Gel Spot Detection and Quantification: How Spot Volume Works

2D Gel Image Alignment Explained: Why, How and What Can Go Wrong

Experimental Design for 2D Gel and 2D-DIGE Studies: A Guide

Zymography Analysis Software | Quantify Zymograms | Phoretix 1D

MaxQuant Alternative for GMP: Validated Proteomics Software

When MaxQuant, Skyline or FragPipe can't pass audit, SpotMap MS can. The validated, 21 CFR Part 11 and Annex 11 alternative to free proteomics tools, built ground-up for regulated host cell protein analysis with native audit trails, electronic signatures and vendor IQ/OQ.

HCP Analysis Software | SpotMap MS by TotalLab

Aligning your LC-MS HCP workflow to USP 1132.1 is a different problem from running the analysis itself. This resource walks through what the chapter asks of your method, why proteomics-based software makes alignment harder, and how SpotMap MS — paired with AuditSafe — gives you USP 1132.1 HCP software that is 21 CFR Part 11 ready from day one.

DeCyder Discontinued: What 2D-PAGE Users Should Use Instead | TotalLab

DeCyder was discontinued by GE Healthcare and is no longer developed or supported. Here is what 2D-DIGE proteomics and HCP coverage labs should migrate to, and how to trial it free on your own images.

Bring HCP Analysis In-House | SpotMap MS by TotalLab

LC-MS HCP Software Comparison: SpotMap MS vs Proteomics Tools

Most LC-MS software your QC team uses today was designed for proteomics, not host cell protein analysis — and it shows. This side-by-side comparison of SpotMap MS against Byos, BioPharma Finder, Genedata Expressionist and MaxQuant looks at the ten dimensions that matter when you're choosing an LC-MS HCP platform for regulated biopharma QC.

Automated Host Cell Protein (HCP) Analysis from LC-MS Data | SpotMap MS

Traditional proteomics software wasn't built for host cell protein analysis. SpotMap MS is. This walkthrough takes you through the fully automated HCP analysis workflow, from raw LC-MS traces and visual quality control through to AI-driven risk assessment, guided peptide validation, and 21 CFR Part 11-compliant threat reporting.

SoftMax Pro Alternative for Pharma QC: PlateLogic Compared | TotalLab

PlateLogic offers vendor-neutral ELISA analysis, 21 CFR Part 11 compliance via AuditSafe, and multi-site standardization. SoftMax Pro, rethought.

Unlocking Trustworthy Fold Change Analysis in 2D Proteomics with SameSpots Software

How to Quantify a Western Blot, Step by Step

The ten steps from blot to publishable number: plan the load, capture an unsaturated image, define lanes and bands, subtract background, measure band volume, normalize, calculate fold change across replicates and report it.

Why AI Can’t Write Your Life Science Software | TotalLab

Generative AI is rapidly changing the lab, but can it write your next compliant product? Discover the right - and wrong - times to use AI code generation in life science software, and why human expertise remains absolutely vital for GMP compliance and data security.

LC-MS HCP Analysis: Methods, ppm Limits and Workflow

Transitioning to mass spectrometry for impurity testing often means drowning in complex data. Learn how SpotMap MS simplifies LC-MS HCP analysis with "hands-free" automated workflows, an AI-categorized threat database, and reporting tools purpose-built for biopharma QC.

Mastering 1D Gel and Western Blot Analysis: A Deep Dive into Normalization with Phoretix 1D

Normalization is the most critical step for achieving accurate, publication-ready quantitative data. In this comprehensive guide, we take a deep dive into the theory and practice of 1D gel and Western blot normalization. Discover the differences between total protein and housekeeping gene methods, and learn how Phoretix 1D software eliminates user bias to automate your entire analysis workflow.

CLIQS 1D Pro Case Studies and Evidence | Real-World 1D Gel Band Matching Results

CLIQS 1D Pro case studies and evidence showing how labs use 1D gel band matching for microbial community fingerprinting and rapid wheat varietal identification.

Case Studies: SameSpots 2D Gel Analysis Software in Leading Proteomics Labs

See how SameSpots 2D gel analysis software helps leading proteomics labs cut analysis time, improve gel alignment and generate more robust biomarker data.

How to Use the Hi3 Peptide Quantification Method for HCP Analysis in SpotMap MS

Learn how to apply Hi3 label-free quantitation in SpotMap MS for accurate, reproducible HCP quantification from LC-MS data.

How SpotMap MS Identifies High-Risk Host Cell Proteins (HCPs) in Biopharmaceutical Analysis

Discover how SpotMap MS automates high-risk HCP identification from LC-MS data using intelligent AI-database matching.

Secure 21 CFR Part 11 & GMP Compliance in Excel Without Macros Using AuditSafe

Relying on Excel macros for 21 CFR Part 11 and GMP compliance exposes your lab to malware, tampering and audit findings. Macro-based plugins are hard to validate, difficult to control and a known cyber attack vector. Discover how TotalLab’s AuditSafe adds secure audit trails, electronic signatures and granular permissions to Excel - delivering compliant, validated workflows without relying on risky VBA code.

How AI Can Transform Modern Pharma QC Environments

Discover how AI-powered, digital CQV platforms help pharma QC teams replace paper-based validation with compliant, data-driven workflows. Learn how to reduce review time, prevent deviations earlier, and align with 21 CFR Part 11 and EU Annex 11.

TotalLab joins Scientist.com as a trusted custom software and OEM development partner

TotalLab is now a Scientist.com supplier, giving pharma and biotech teams an easier, compliant route to custom life science and OEM software development.

Case Studies Demonstrating SpotMap MS for LC-MS Host Cell Protein (HCP) Analysis

Explore detailed case studies, posters, and testimonials highlighting the performance and reliability of SpotMap MS software. Designed for automated LC-MS based host cell protein (HCP) analysis, SpotMap MS is trusted by pharmaceutical researchers for accuracy, reproducibility, and ease of use. Use these resources to confidently evaluate how SpotMap MS can support your lab’s QC and research workflows.

How to Navigate AI-Based 21 CFR Part 11/GMP Compliance

The AI regulatory landscape is evolving rapidly, creating complex compliance challenges for organisations. This guide helps TotalLab clients navigate the EU AI Act, UK's pro-innovation approach and sector-specific requirements. Learn how TotalLab can help with your risk assessment, documentation, governance and building compliant AI systems from the ground up.

SpotMap MS Ion Intensity Maps for LC-MS Quality Control in Pharma

SpotMap MS empowers pharmaceutical analysis of host cell proteins via LC-MS QC with advanced ion intensity maps for rapid detection of sample issues, ensuring reliable and compliant data.

GelAnalyzer vs Phoretix 1D: what the free gel analyzer does, and when to move on

GelAnalyzer is a free 1D gel analyzer that handles a single gel well. This guide covers what version 26.1.1 does, what the paid Plus tier adds, and the three places quantitative western blot work outgrows it: 8-bit images, normalization to a loading control, and records for regulated labs.

Immunoaffinity Chromatography (IAC) for HCP Coverage Determination

Immunoaffinity chromatography enhances detection and purification of host cell proteins, delivering reliable results for biopharmaceutical quality control.

Phoretix 1D User Manual/Guide

Are you currently using or trialing a copy of TotalLab's Phoretix 1D SDS-PAGE analysis software? Find a full user manual/guide here.

Host Cell Protein Analysis: ELISA, 2D and LC-MS Methods

Host Cell Protein (HCP) impurity analysis is essential for safe biologics manufacturing. Discover how TotalLab’s software tools help to streamline HCP quantification when using gold-standard techniques like ELISA, 2D-PAGE, and LC-MS to support regulatory compliance and therapeutic safety.

Why Do I Need to Know My HCP Antibody Coverage?

Understanding your HCP antibody coverage is essential to validating your ELISA for host cell protein detection. This article explains how coverage impacts assay reliability, regulatory compliance, and effective antibody selection in biologics and biosimilar development.

2D Gel Spot Cutting and Picking for Protein Identification by Mass Spec

Learn how TotalLab software supports accurate, contamination-free 2D protein spot excision and downstream mass spectrometry analysis. From 2D-DIGE to Western blot workflows, our tools streamline detection, quantification, and protein ID.

PDQuest Discontinued: Bio-Rad Recommends TotalLab’s SameSpots

Following the discontinuation of Bio-Rad's PDQuest software, Bio-Rad now recommends TotalLab’s SameSpots and SpotMap 2D as trusted replacements for 2D gel image analysis and HCP antibody validation. Learn how these solutions offer modern workflows for differential expression and coverage scoring.

Pattern Matching & Dendrogram Generation in CLIQS 1D Pro

Automate your 1D gel band matching and dendrogram generation with CLIQS 1D Pro. Build searchable gel databases and accelerate your electrophoresis pattern analysis.

Imaging 2D Gels: Resolution, Bit Depth and Dynamic Range

Discover expert insights on 2D gel electrophoresis imaging—a critical step in proteomic analysis. Learn best practices for high-resolution gel imaging, dynamic range optimization, and artifact prevention to ensure accurate, reproducible data. Brought to you by TotalLab, innovators in 2D proteomic analysis software.

Equipment & Reagents Required for Pulsed Field Gel Electrophoresis (PFGE)

Explore TotalLab's advanced PFGE equipment list designed for life scientists. Discover how our pulsed-field gel electrophoresis systems can deliver precise DNA separation for your research needs

HCP Coverage Analysis Using 2D Western Blot

Discover how 2D Western blotting enhances Host Cell Protein (HCP) coverage analysis in biopharmaceutical research. Learn the key steps, from protein separation and transfer to PVDF membranes to antibody staining and data analysis. See how TotalLab's SpotMap software improves HCP detection and quantification, ensuring regulatory compliance and accurate results.

TotalLab’s SpotMap 2D: Automated 2D Western Blot Analysis Software for HCP Detection

Discover SpotMap: automated 2D Western blot analysis software for host cell protein detection. Enhance accuracy and streamline gel image workflows.

How to Calculate Western Blot Normalization (With Examples)

Learn how to calculate Western blot normalization, compare HKP and total protein methods, and boost accuracy in protein quantitation with TotalLab's Phoretix 1D software.

Precipitin test: how it works, the main types and how to measure the results

The precipitin test detects an antigen or antibody by the visible precipitate they form together. How the reaction works, the ring test, Ouchterlony and radial immunodiffusion, its forensic and clinical uses, and how to measure rings, lines and rockets from an image.

Dot blot protocol: how to run a dot blot and read the results

A dot blot protocol you can follow, with sample amounts, spotting volumes, incubation times and the controls that make the result readable. Then how to read the spots, turn them into numbers, compare a dot blot with a western blot, and fix the common problems.

DNA microarray: what it is, how it works and how to analyze the images

A DNA microarray measures thousands of DNA or RNA sequences at once by hybridizing a labeled sample to spots of known probes. How it works step by step, the main types, what the results mean, how it compares with RNA-seq, and how the scanned image is turned into numbers.

What is Host Cell Protein?

Discover what host cell proteins (HCPs) are, why they matter in biologic drug development, and how they’re analyzed for safety. Learn about common HCP analysis methods, challenges, and strategies to manage risks, with insights on tools from Totallab

How to read a western blot: what each band is telling you

Read a western blot one question at a time: is the band the right size, is it the only band, did every lane load the same amount, can the band be measured, and how much did it change between samples. With an annotated example blot and a worked fold-change calculation.

Verified Case Studies and Evidence Demonstrating SpotMap 2D for Host Cell Protein Coverage

Explore detailed case studies, posters, and testimonials highlighting the performance and reliability of SpotMap 2D software. Designed for automated 2D-PAGE host cell protein coverage analysis, SpotMap 2D is trusted by pharmaceutical researchers for accuracy, reproducibility, and ease of use. Use these resources to confidently evaluate how SpotMap 2D can support your lab’s QC and research workflows.

Western blot and SDS-PAGE images: how to capture, edit and present them

How to get a western blot or SDS-PAGE image you can quantify and publish: 16-bit capture without saturation, the right file format, the edits journals allow and the ones they do not, and how to label and present the figure.

TotalLab and Merck Collaborate to Automate 2D Gel Electrophoresis

By combining our industry leading SameSpots and SpotMap software with their Auto2D hardware, Merck have been able to rapidly reduce the time taken for complete 2D based experiments including proteomic/HCP analysis. This combination increases throughput by introducing high levels of automation whilst simultaneously reducing inter-operator variability.

2D Gel Electrophoresis: Principle, Steps and Applications

Learn how 2D electrophoresis can separate proteins by isoelectric point and molecular weight, aiding in analysis and research. Perfect for understanding complex protein mixtures and identifying biomarkers.

Bacterial Community Fingerprinting Protocol

Bacterial community fingerprinting refers to a number of cultivation-independent methods that are used to measure biodiversity in environmental samples or to profile microbial community structures, e.g. in response to experimental conditions. Read this guide to understand how you can use CLIQS 1D Pro in your bacterial fingerprinting studies.

2D-SDS PAGE Analysis Methods For Determining HCP Coverage Using Process Derived anti-HCP Polyclonal Antibodies

Here we present the characterization of a process specific anti-Pichia pastoris HCP antibody using 2 different analysis platforms: Biorad’s PDQuest and TotalLab’s SpotMap.

ALCOA & ALCOA+ Principles Explained | Pharma Data Integrity Guide

Discover the essential ALCOA principles in life sciences and pharmaceutical production. Learn how Attributable, Legible, Contemporaneous, Original, and Accurate guidelines ensure data integrity, regulatory compliance, and patient safety. Understand the extended ALCOA+ principles and their critical role in the industry

Western Blot Troubleshooting: What Your Blot Is Telling You

Find your western blot problem by what it looks like, from high background and smeared bands to no signal, extra bands, smiling lanes and saturation. Get the likely causes and the first fix, and find out whether you can still quantify the blot or need to run it again.

Case Study: WPI Adds 21 CFR Part 11 to EVOM with AuditSafe

How to Implement 21 CFR Part 11 In Your Lab

Learn how TotalLab's software implements secure electronic records, robust audit trails, and user authentication protocols. Achieve compliance seamlessly with our expert guidance

Background Subtraction for 1D SDS-PAGE & Western Blot Analysis | Phoretix 1D

Uneven backgrounds ruining your gel quantification? Learn how to choose the right background subtraction method for SDS-PAGE and Western blots using Phoretix 1D software.

HCP Antibody Coverage: 2D Western Blot vs AAE vs ELISA-MS

Explore the current landscape of anti-HCP antibody coverage with our article comparing 2D DIGE, ELISA, and AAE. Optimise your antibody selection process for robust anti-HCP analysis in biopharmaceutical research.

2D-DIGE vs LC-MS/MS: Strengths, Limitations, When to Use Each

Dive into the world of precision and versatility as we explore the distinct advantages offered by 2D DIGE and LC-MS/MS for comprehensive proteomic profiling.

2D-DIGE vs 2D Gel Electrophoresis: What DIGE Is and When to Use It

In this short guide, we'll be explaining to you the technical process of performing 2D DIGE experiments and some of the advantages of using the technique over standard 2D electrophoresis.

CLIQS 1D Pro | How to create dendrograms for similarity

CLIQS 1D Pro allows the building of a database of lanes and bands extracted from images of 1D gels and blots. Here we demonstrate how to visualise the similarities between lanes in the form of dendrogams or similarity tables.

SameSpots | How to assign protein isoelectric point and molecular weight to spots

Learn how to add pI and MW info into SameSpots for automatic calculation of molecular weight for all identified spots.

CLIQs 1D Pro | How to Accurately Match Bands/Compare Lanes Across Different Gels and Blots

Watch how CLIQS 1D Pro can perform a simple comparison between lanes taken from different gels or blots, to identify any matches between them.

How to Calculate Host Cell Protein (HCP) Antibody Coverage % | SpotMap

This tutorial will show you how to analyse 2D gel electrophoresis and western blot images using TotalLab's SpotMap HCP image analysis software and calculate a percentage coverage score.

Phoretix 1D | How to Choose the Correct Background Removal Method

In this demo, we explain the difference between our background removal techniques and how to choose the correct one based on your data.

How to Automate Your Western Blot or Gel Electrophoresis Analysis

The automatic analysis features built into Phoretix 1D can save you huge amounts of time in a high-throughput environment and minimise inter-operator and inter-lab variability.

Phoretix 1D | How to Analyse Thin Layer Chromatography (TLC) Experiments

This tutorial will show you how to analyze thin layer chromatography slides/images using TotalLab's Phoretix 1D image analysis software.

CLIQS 1D Pro Image Database Software | Tutorial Series | How to Match Bands Across Your Database

In this video we show you how to perform a search of your blot or gel database to find matching bands across lanes, how to fine-tune your search parameters and how to express your matches statistically.

Phoretix 1D | How to Analyse a Western Blot

Following the launch of our Phoretix 1D image analysis software we've put together this tutorial video to show you how to analyse gel electrophoresis and blot images.

CLIQS 1D Pro Image Database Software | Tutorial Series | How to Save Sets of Lanes for Matching

In this video we'll be showing you how to create a set or group of existing lanes that you can repeatedly match across your entire 1D gel or Western blot database.

CLIQS 1D Pro Image Database Software | Tutorial Series | How to Create Lanes for Band Matching

In this video, we'll be showing you how to select an existing lane or create a new lane containing the bands you're interested in matching across your entire 1D gel or Western blot database.

CLIQS 1D Pro Image Database Software | Tutorial Series | How to Create a Database of Gel/Blot Images

In this video, we'll guide you through the first step in using our CLIQS 1D Pro software - the creation of a database containing lanes and bands extracted from 1D gels and blots analysed using our CLIQS 1D software.

SameSpots 2D Image Analysis Software | Tutorial Series | Image Quality Control

This video will show you the tools that are built directly into SameSpots to critically evaluate the quality of your 2D images.

SameSpots 2D Image Analysis Software | Tutorial Series | Multivariate Statistical Analysis of Spots

This video guides users through the statistical analysis of spots within 2D gels and Western blots using our SameSpots software.

SameSpots 2D Image Analysis Software | Tutorial Series | How to Align Images (Automatic & Manual)

This video outlines how SameSpots's next-generation image alignment algorithm is utilised to perfectly align 2D gel and Western blot images for statistical analysis in proteomic work.

Problem solving with SpotMap

Our guide covers some of the problems you can overcome when using our SpotMap software. It provides an introduction to key features, image QC, image analysis and details on the analysis element of the software.

How to Analyze 2D Gels: The SameSpots Workflow Step by Step

Discover the key steps of the SameSpots workflow and how it allows you to analyse 2D gels with any type of staining.

P-values, FDR and q-values Explained, With a Worked Example

In this article we explore p-values, q-values and false discovery rates through example experiment results.

How to configure system security in Windows for GxP compliance

If you're operating in a 21 CFR part 11 compliance laboratory then setting up Windows security becomes a major part in setting up your system. Take a look at our tips.

Tips for setting up your electronic signature for the FDA

We have created these guidelines to support you in setting up your electronic signatures for FDA CFR part 11 compliance.

21 CFR Part 11 Compliance Guide

Compliance with FDA 21 CFR Part 11 is critical for life science laboratories relying on electronic records and signatures. In this comprehensive technical guide, we break down how our AuditSafe software helps users achieve the regulatory requirements of Subpart B, EU Annex 11, GMP and ALCOA data integrity principles. Download the guide to discover how TotalLab's AuditSafe software seamlessly enforces compliance and secures your digital workflows.

What Are Electronic Signatures for 21 CFR/GMP Compliance?

This guide provides on how you can use AuditSafe can ensure your electronic signatures are generated in compliance with 21 CFR Part 11/GMP regulations.

SpotMap | How to align Western blots to 2D gel images

Understanding when alignment is correctly implemented is easy in SpotMap as there are visual identifiers in the software that indicate when images are ready for analysis.

How to Correctly Align 2D Gels and Western Blots for HCP Analysis

Alignment can be changed and corrected at any point on the analysis however there are four ways to check you have Align your images correctly.

21 CFR part 11/GMP compliance checklist

We have created this 21 CFR part 11 compliance checklist to ensure you are have the right checks in place to comply with the regulations.