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Mass Spectrometry

An analytical technique that measures the mass-to-charge ratio of ions. The purpose is to identify the amount and type of chemicals present in a sample by measuring the mass-to-charge ratio and abundance of gas-phase ions.

Workflows requiring Mass Spectrometry:

Methods for performing Mass Spectrometry:


MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization – Time of Flight)

MALDI-TOF is a “soft ionization” technique, ideal for analyzing large biomolecules like proteins and peptides without causing fragmentation. By mixing the sample with a matrix and using a laser pulse, it ionizes the sample. Its key differentiator is its ability to rapidly analyze large molecules, making it especially useful in proteomics and microbial identification.

Electrospray Ionization (ESI)

ESI operates by passing a sample solution through a high-voltage needle, creating charged droplets that produce ions. Its versatility stands out, as it can ionize a broad range of compounds, from small molecules to large proteins. ESI’s compatibility with Liquid Chromatography (LC) allows for seamless separation and subsequent MS analysis, making it a go-to for metabolomics and lipidomics.

Tandem Mass Spectrometry (MS/MS)

MS/MS is a two-stage process where ions are first separated, selected ions are fragmented, and then the fragments are analyzed. Its strength lies in providing detailed structural information, especially for peptides. By targeting specific ions and monitoring their fragments, MS/MS offers unparalleled specificity and precision, making it invaluable for proteomics and pinpoint quantitative analysis.

Mass Spectrometry Sample Prep

The process of preparing biological samples for analysis by mass spectrometry (MS). This involves extracting, purifying, and concentrating the molecules of interest from a complex mixture. The main purpose is to ensure that the sample is in a suitable form for MS analysis, free from contaminants that might interfere with the MS readings, and concentrated enough to be detected.

How to Automate the Mass Spectrometry Sample Prep process:

Mass Spectrometry Sample Prep has never been easier

The OT-2 is a bench-top liquid handler designed to be accessible and flexible enough to automate many common applications.

Benefits of Automation over Manual Pipetting for Mass Spectrometry Sample Prep:

Resource Spotlights

Opentrons helps you automate Mass Spectrometry Sample Prep with open-source protocols for the OT-2 and Opentrons Flex

Mass Spectrometry Hyphenated Techniques


Gas Chromatography-Mass Spectrometry (GC-MS)

GC-MS specializes in analyzing volatile and thermally stable compounds. Fusing the separation capabilities of gas chromatography with the identification prowess of mass spectrometry, it’s commonly employed in forensics, environmental monitoring, and flavor profiling. Its strength lies in the precise identification of organic compounds using well-established libraries.

Liquid Chromatography-Mass Spectrometry (LC-MS)

LC-MS extends the applicability of mass spectrometry to thermally labile and non-volatile compounds. By integrating the broad separation power of liquid chromatography with detailed mass spectrometric analysis, it becomes invaluable in proteomics, drug development, and metabolite profiling. It stands out for its ability to handle larger and diverse molecules, bridging gaps left by GC-MS.

Overview Gas chromatography coupled with mass spectrometry Liquid chromatography coupled with mass spectrometry
Sample Type Volatile and thermally stable compounds Non-volatile and thermally labile compounds
Ionization Techniques Electron Impact (EI), Chemical Ionization (CI) Electrospray Ionization (ESI), Atmospheric Pressure Chemical Ionization (APCI)
Applications Forensics, environmental monitoring, drug testing, flavor profiling Proteomics, drug development, metabolite profiling
Complexity & Maintenance Moderate; maintenance due to column and MS conditions Higher; potential column clogging and contamination
Resolution High (dependent on column and instrument) High (dependent on column and instrument)
Typical Uses Drug testing, environmental pollutants, metabolomics Biomolecules, peptides, pharmaceuticals, large organic molecules
Detector Sensitivity High for volatile compounds High, especially with modern detectors and for a broader range of compounds
Advantages Effective for a wide range of volatile organic compounds, established method with well-defined libraries Broad applicability, can handle larger and more diverse compounds
Limitations Limited to volatile and thermally stable compounds, potential fragmentation upon ionization can complicate spectra Potential for sample loss or degradation due to multiple steps, sensitivity can be affected by matrix effects

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