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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Updated: Jun 6, 2026

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Published on: June 8, 2020

Laboratory data and sample management for proteomics.

Jari Häkkinen¹, Fredrik Levander

¹Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden.

Methods in Molecular Biology (Clifton, N.J.)

|November 11, 2010

Summary

This summary is machine-generated.

Managing large proteomics data is challenging. A laboratory information management system (LIMS), like Proteios Software Environment (ProSE), can streamline proteomics workflows and data handling.

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Last Updated: Jun 6, 2026

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Area of Science:

Proteomics
Bioinformatics
Laboratory Management

Background:

Proteomic experiments generate vast amounts of diverse data, posing significant handling challenges.
Effective management of samples, data, and annotation information is crucial for successful proteomics research.
Existing data handling methods can be cumbersome, hindering efficient experimental progression.

Purpose of the Study:

To discuss the critical role of a Laboratory Information Management System (LIMS) in addressing data handling challenges in proteomics.
To demonstrate practical applications of the Proteios Software Environment (ProSE) for managing proteomics workflows.
To provide step-by-step examples of ProSE usage for distinct proteomics experimental pipelines.

Main Methods:

Literature review on LIMS in proteomics.
Case study analysis of Proteios Software Environment (ProSE).
Development of step-by-step usage examples for two distinct proteomics workflows within ProSE.

Main Results:

A LIMS, specifically ProSE, can effectively centralize and manage proteomic sample and data information.
ProSE facilitates the integration of experimental data with sample metadata and annotations.
Demonstrated successful application of ProSE in handling two different proteomics workflows, simplifying data management.

Conclusions:

Laboratory Information Management Systems (LIMS) are essential tools for overcoming data handling complexities in modern proteomics.
The Proteios Software Environment (ProSE) offers a viable solution for efficient management of proteomics data and workflows.
Implementing ProSE can significantly improve the organization and accessibility of data in proteomics laboratories.