LCMS
More information
WebinarsAbout usContact usTerms of use
LabRulez s.r.o. All rights reserved. Content available under a CC BY-SA 4.0 Attribution-ShareAlike
Author
DataApex
DataApex
Since 1991 DataApex develops and manufactures chromatography data stations. DataApex is constantly striving to provide users with efficient and up-to-date tools for chromatography data processing.
Tags
Article
Video
Software
Product
LinkedIn Logo

Clarity Tutorial - Instrument window - Overview

Tu, 30.12.2025
| Original article from: DataApex
A clear overview of the Instrument Window in Clarity Chromatography Software, explaining interface layout, workflow icons, analysis control, chromatogram handling, and calibration.
Video placeholder
  • Photo: DataApex: Clarity Tutorial - Instrument window - Overview
  • Video: DataApex: Clarity Tutorial - Instrument window - Overview

Introduction

This article provides a detailed, structured explanation of the Instrument Window in Clarity Chromatography Software, as demonstrated in the referenced video tutorial. The Instrument Window is the central operational interface used for method setup, acquisition control, monitoring, data evaluation, and calibration.

General Layout of the Instrument Window

The Instrument Window is divided into three main sections, each serving a distinct role in the chromatographic workflow:

  1. Simplified Workflow Icons
  2. Analysis Status and Acquisition Control Bar
  3. Information Table for the Running Analysis

Together, these sections provide a streamlined overview of the entire analytical process—from method configuration to data processing.

Section 1: Simplified Workflow Icons

The upper portion of the Instrument Window contains a series of icons representing a simplified, logical chromatographic workflow. Each icon opens a dedicated dialog or window related to a specific step of the analysis.

Method Setup

  • Opens the Method Setup dialog
  • Allows users to browse through multiple configuration tabs
  • Used to define all parameters required for measurement (instrument settings, detector configuration, timing, etc.)

This is the primary starting point for defining how an analysis will be performed.

Single Analysis and Sequence Setup

  • Provides access to Single Analysis and Sequence dialogs
  • Enables configuration of:
    • Individual measurements
    • Automated sequences consisting of multiple samples

These dialogs are used to define what will be measured and in what order.

Device Monitor

  • Displays a dedicated section for each configured instrument
  • Shows the current operational state of instruments
  • Allows real-time supervision of system readiness and status

This function is essential for verifying that all hardware components are correctly configured and operational.

Data Acquisition (Signal Monitoring)

  • Opens the Data Acquisition dialog
  • Enables real-time monitoring of detector signals
  • Allows users to observe live chromatographic responses during analysis

This feature is particularly useful during method development, troubleshooting, or system verification.

Chromatogram Window

  • Provides access to measured chromatograms
  • Used for:
    • Viewing chromatographic data
    • Evaluating peak shapes and retention times
    • Performing data interpretation tasks

This is the primary environment for post-acquisition data review.

Calibration

  • Opens the Calibration Window
  • Used to set up and manage calibrations
  • Supports quantitative evaluation by linking signal response to concentration

Calibration is a critical step for ensuring accurate and reproducible quantitative results.

Section 2: Analysis Status and Acquisition Control

The second major section of the Instrument Window is the Analysis Status Bar, which provides immediate feedback on the system and analysis state.

Key Functions

  • Displays the current status of the instrument
  • Shows whether the system is idle, running, or in another operational state
  • Contains acquisition control buttons to:
    • Start analyses
    • Stop or control data acquisition

This section acts as the operational control center during routine work.

Section 3: Information Table

The third section is an Information Table that displays details about the currently running analysis.

Displayed Information

  • Current analysis status
  • Relevant runtime information
  • Contextual data linked to the active measurement

This table provides users with a concise overview of ongoing activities without needing to open additional dialogs.

Project, Batch Processing, and User Settings

In addition to direct analytical functions, the Instrument Window also provides access to broader data and workflow management tools.

Project Management

  • Allows users to manage the current project
  • Ensures all methods, analyses, and results are grouped consistently

Batch Processing

  • Opens the Batch dialog
  • Enables processing of multiple chromatograms simultaneously
  • Useful for reprocessing data or applying consistent evaluation parameters

Data Export Management

  • Controls how data are exported from the software
  • Supports customization of export formats and workflows

User Settings

  • Allows modification of user-specific settings
  • Settings are:
    • Bound to the individual user
    • Stored within the user’s desktop file

This ensures a personalized working environment without affecting other users.

Practical Workflow Summary

In daily laboratory operation, the Instrument Window supports the following logical sequence:

  1. Define the method using Method Setup
  2. Configure samples via Single Analysis or Sequence
  3. Verify system readiness in Device Monitor
  4. Monitor signals in Data Acquisition
  5. Evaluate results in the Chromatogram Window
  6. Apply or refine Calibration
  7. Manage data through Batch Processing and Export

Conclusion

The Instrument Window in Clarity Chromatography Software serves as a centralized and highly structured interface that integrates method configuration, instrument control, real-time monitoring, data evaluation, and project management.

By organizing complex chromatographic tasks into clearly defined sections and workflow-driven icons, the software enables efficient and intuitive laboratory operation. Understanding the role of each component within the Instrument Window is essential for both routine analyses and advanced method development.

DataApex
LinkedIn Logo
 

Related content

Analysis of Anti-Degradant Additive (6PPD) and its Transformation Product 6PPD-Quinone in Tire Rubber Using an Integrated HPLC System

Applications
| 2026 | Shimadzu
Instrumentation
HPLC
Manufacturer
Shimadzu
Industries
Energy & Chemicals

Performance Evaluation of Microbial Identification Using a Benchtop MALDI-TOF MS

Applications
| 2026 | Shimadzu
Instrumentation
MALDI, LC/MS, LC/TOF, Software
Manufacturer
Shimadzu
Industries
Pharma & Biopharma, Food & Agriculture

A Combined Method for Anionic, Cationic, and Zwitterionic PFAS using a Direct Injection UPLC™-MS/MS Method for Environmental Water Samples

Applications
| 2026 | Waters
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Waters
Industries
Environmental

Beyond the box: A ready-to-run workflow for quantitating 80 drugs of abuse in whole blood with the TSQ Certis Triple Quadrupole MS

Applications
| 2026 | Thermo Fisher Scientific
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Thermo Fisher Scientific
Industries
Forensics

Mastering Single Cell Proteomics: Daily Excellence with μPAC Neo Plus Trap-and-Elute Workflow

Presentations
| 2026 | Thermo Fisher Scientific
Instrumentation
HPLC, LC/Orbitrap, LC/MS, LC/MS/MS
Manufacturer
Thermo Fisher Scientific
Industries
Proteomics
 

Related articles

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction
Article | Events

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction

ISC 2026 Short Course 7 explores supercritical fluid extraction (SFE) and chromatography (SFC), from CO₂ fundamentals to analytical and preparative applications.
International Symposium on Chromatography - (ISC)
tag
share
more
Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer
Article | Product

Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer

A new paradigm in steroid quantification. Thermo Scientific Stellar MS combines PRM, MS³, and dual HCD/CID fragmentation to enhance sensitivity, selectivity, and method development efficiency.
Thermo Fisher Scientific
tag
share
more
You talk, we understand – The way out of the tower of Babel
Article | Science and research

You talk, we understand – The way out of the tower of Babel

Why a shared metrology vocabulary matters in analytical laboratories. This Eurachem guide clarifies key terms, reduces misunderstandings, and supports reliable, fit-for-purpose measurement results.
Eurachem
tag
share
more
LabRulez at analytica 2026
Article | Events

LabRulez at analytica 2026

Meet LabRulez at analytica 2026 in Munich - A1.506. Explore live portal demos, discover marketplace instruments and spare parts, and learn how our online platforms support analytical chemistry professionals.
LabRulez
tag
share
more
 

Related content

Analysis of Anti-Degradant Additive (6PPD) and its Transformation Product 6PPD-Quinone in Tire Rubber Using an Integrated HPLC System

Applications
| 2026 | Shimadzu
Instrumentation
HPLC
Manufacturer
Shimadzu
Industries
Energy & Chemicals

Performance Evaluation of Microbial Identification Using a Benchtop MALDI-TOF MS

Applications
| 2026 | Shimadzu
Instrumentation
MALDI, LC/MS, LC/TOF, Software
Manufacturer
Shimadzu
Industries
Pharma & Biopharma, Food & Agriculture

A Combined Method for Anionic, Cationic, and Zwitterionic PFAS using a Direct Injection UPLC™-MS/MS Method for Environmental Water Samples

Applications
| 2026 | Waters
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Waters
Industries
Environmental

Beyond the box: A ready-to-run workflow for quantitating 80 drugs of abuse in whole blood with the TSQ Certis Triple Quadrupole MS

Applications
| 2026 | Thermo Fisher Scientific
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Thermo Fisher Scientific
Industries
Forensics

Mastering Single Cell Proteomics: Daily Excellence with μPAC Neo Plus Trap-and-Elute Workflow

Presentations
| 2026 | Thermo Fisher Scientific
Instrumentation
HPLC, LC/Orbitrap, LC/MS, LC/MS/MS
Manufacturer
Thermo Fisher Scientific
Industries
Proteomics
 

Related articles

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction
Article | Events

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction

ISC 2026 Short Course 7 explores supercritical fluid extraction (SFE) and chromatography (SFC), from CO₂ fundamentals to analytical and preparative applications.
International Symposium on Chromatography - (ISC)
tag
share
more
Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer
Article | Product

Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer

A new paradigm in steroid quantification. Thermo Scientific Stellar MS combines PRM, MS³, and dual HCD/CID fragmentation to enhance sensitivity, selectivity, and method development efficiency.
Thermo Fisher Scientific
tag
share
more
You talk, we understand – The way out of the tower of Babel
Article | Science and research

You talk, we understand – The way out of the tower of Babel

Why a shared metrology vocabulary matters in analytical laboratories. This Eurachem guide clarifies key terms, reduces misunderstandings, and supports reliable, fit-for-purpose measurement results.
Eurachem
tag
share
more
LabRulez at analytica 2026
Article | Events

LabRulez at analytica 2026

Meet LabRulez at analytica 2026 in Munich - A1.506. Explore live portal demos, discover marketplace instruments and spare parts, and learn how our online platforms support analytical chemistry professionals.
LabRulez
tag
share
more
 

Related content

Analysis of Anti-Degradant Additive (6PPD) and its Transformation Product 6PPD-Quinone in Tire Rubber Using an Integrated HPLC System

Applications
| 2026 | Shimadzu
Instrumentation
HPLC
Manufacturer
Shimadzu
Industries
Energy & Chemicals

Performance Evaluation of Microbial Identification Using a Benchtop MALDI-TOF MS

Applications
| 2026 | Shimadzu
Instrumentation
MALDI, LC/MS, LC/TOF, Software
Manufacturer
Shimadzu
Industries
Pharma & Biopharma, Food & Agriculture

A Combined Method for Anionic, Cationic, and Zwitterionic PFAS using a Direct Injection UPLC™-MS/MS Method for Environmental Water Samples

Applications
| 2026 | Waters
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Waters
Industries
Environmental

Beyond the box: A ready-to-run workflow for quantitating 80 drugs of abuse in whole blood with the TSQ Certis Triple Quadrupole MS

Applications
| 2026 | Thermo Fisher Scientific
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Thermo Fisher Scientific
Industries
Forensics

Mastering Single Cell Proteomics: Daily Excellence with μPAC Neo Plus Trap-and-Elute Workflow

Presentations
| 2026 | Thermo Fisher Scientific
Instrumentation
HPLC, LC/Orbitrap, LC/MS, LC/MS/MS
Manufacturer
Thermo Fisher Scientific
Industries
Proteomics
 

Related articles

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction
Article | Events

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction

ISC 2026 Short Course 7 explores supercritical fluid extraction (SFE) and chromatography (SFC), from CO₂ fundamentals to analytical and preparative applications.
International Symposium on Chromatography - (ISC)
tag
share
more
Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer
Article | Product

Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer

A new paradigm in steroid quantification. Thermo Scientific Stellar MS combines PRM, MS³, and dual HCD/CID fragmentation to enhance sensitivity, selectivity, and method development efficiency.
Thermo Fisher Scientific
tag
share
more
You talk, we understand – The way out of the tower of Babel
Article | Science and research

You talk, we understand – The way out of the tower of Babel

Why a shared metrology vocabulary matters in analytical laboratories. This Eurachem guide clarifies key terms, reduces misunderstandings, and supports reliable, fit-for-purpose measurement results.
Eurachem
tag
share
more
LabRulez at analytica 2026
Article | Events

LabRulez at analytica 2026

Meet LabRulez at analytica 2026 in Munich - A1.506. Explore live portal demos, discover marketplace instruments and spare parts, and learn how our online platforms support analytical chemistry professionals.
LabRulez
tag
share
more
 

Related content

Analysis of Anti-Degradant Additive (6PPD) and its Transformation Product 6PPD-Quinone in Tire Rubber Using an Integrated HPLC System

Applications
| 2026 | Shimadzu
Instrumentation
HPLC
Manufacturer
Shimadzu
Industries
Energy & Chemicals

Performance Evaluation of Microbial Identification Using a Benchtop MALDI-TOF MS

Applications
| 2026 | Shimadzu
Instrumentation
MALDI, LC/MS, LC/TOF, Software
Manufacturer
Shimadzu
Industries
Pharma & Biopharma, Food & Agriculture

A Combined Method for Anionic, Cationic, and Zwitterionic PFAS using a Direct Injection UPLC™-MS/MS Method for Environmental Water Samples

Applications
| 2026 | Waters
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Waters
Industries
Environmental

Beyond the box: A ready-to-run workflow for quantitating 80 drugs of abuse in whole blood with the TSQ Certis Triple Quadrupole MS

Applications
| 2026 | Thermo Fisher Scientific
Instrumentation
LC/MS, LC/MS/MS, LC/QQQ
Manufacturer
Thermo Fisher Scientific
Industries
Forensics

Mastering Single Cell Proteomics: Daily Excellence with μPAC Neo Plus Trap-and-Elute Workflow

Presentations
| 2026 | Thermo Fisher Scientific
Instrumentation
HPLC, LC/Orbitrap, LC/MS, LC/MS/MS
Manufacturer
Thermo Fisher Scientific
Industries
Proteomics
 

Related articles

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction
Article | Events

ISC 2026 Short Course 7 - Supercritical Fluids in Chromatography and Extraction

ISC 2026 Short Course 7 explores supercritical fluid extraction (SFE) and chromatography (SFC), from CO₂ fundamentals to analytical and preparative applications.
International Symposium on Chromatography - (ISC)
tag
share
more
Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer
Article | Product

Advancing Steroid Quantification: Unlocking Sensitivity and Selectivity with the Thermo Scientific Stellar Mass Spectrometer

A new paradigm in steroid quantification. Thermo Scientific Stellar MS combines PRM, MS³, and dual HCD/CID fragmentation to enhance sensitivity, selectivity, and method development efficiency.
Thermo Fisher Scientific
tag
share
more
You talk, we understand – The way out of the tower of Babel
Article | Science and research

You talk, we understand – The way out of the tower of Babel

Why a shared metrology vocabulary matters in analytical laboratories. This Eurachem guide clarifies key terms, reduces misunderstandings, and supports reliable, fit-for-purpose measurement results.
Eurachem
tag
share
more
LabRulez at analytica 2026
Article | Events

LabRulez at analytica 2026

Meet LabRulez at analytica 2026 in Munich - A1.506. Explore live portal demos, discover marketplace instruments and spare parts, and learn how our online platforms support analytical chemistry professionals.
LabRulez
tag
share
more
Other projects
GCMS
ICPMS
Follow us
FacebookX (Twitter)LinkedInYouTube
More information
WebinarsAbout usContact usTerms of use
LabRulez s.r.o. All rights reserved. Content available under a CC BY-SA 4.0 Attribution-ShareAlike