Developments in mass spectrometry have enabled a new level of accuracy and sensitivity in protein analysis. However, achieving reliable results requires meticulous sample preparation tailored to each experiment’s goals and challenges. Without careful planning, issues such as contamination and protein degradation can compromise outcomes.
This guide offers essential insights into preparing high-quality samples for mass spectrometry.
Download this guide to explore:
- Comprehensive workflows for effective protein analysis
- Techniques to optimize protein extraction and digestion
- Key quality control measures for consistent results
How To Guide
Perfect Your Protein Prep for Mass
Spectrometry
Kaja Ritzau-Reid, PhD
Mass spectrometry (MS) is a versatile and powerful technique for proteomics. In the last decade, rap
id
developments in MS instrumentation and methodologies have provided a new level of accuracy and
sensitivity in protein analysis, opening up new applications in biological research, biopharmaceuticals and
diagnostics.
1,2
A well-designed MS experiment can identify and quantify unknown compounds in a biological sample.
However, it is important to ensure the quality and reliability of your MS results by taking the time to plan
your experiment and prepare a high-quality sample.
Biological samples are complex and there is no gold standard for sample preparation. Protocols will
differ depending on your sample type and experimental goals, with it important to understand the differ
ent
options that are available for you to optimize your workflow. This guide provides some essential tips
and tricks to help you as you plan your MS experiment; from workflow optimization to practical tips about
equipment use, quality control measures and choosing the right analytical method.
Guiding principles
Top-down or bottom-up?
Two fundamental strategies are used in protein identification by MS: top-down and bottom-up. In top
down
analysis, intact proteins are separated from complex biological samples and analyzed in their
intact form. This can be a useful technique for the analysis of single proteins. The bottom-up, or “shotgun”
approach, however, is still considered the mainstay of proteomic analysis and is used to identify unknown
protein components in a sample. Proteins are digested into peptides, separated via liquid chromatogra
phy
(LC) and analyzed by MS.3 We will focus on bottom-up strategy in this guide.
3
Key considerations before you start
Taking the time to properly plan your experiment before diving into lab work is the simplest way to get on
the right track for experimental success.
1
