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A sample is injected into the mass spectrometer, and the molecules are ionized and accelerated.

MS has become invaluable across a broad range of fields and applications, including proteomics.

The development of high-throughput and quantitative MS proteomics workflows within the last two decades has expanded the scope of what we know about protein structure, function, modification and global protein dynamics.

This overview outlines the role of mass spectrometry in the field of proteomics, reviews MS methodology and instrumentation, and touches on sample preparation and liquid chromatographybased separation prior to MS analysis.

Genomics and proteomics are considerably more difficult to study together than genomics or even transcriptomics alone, because of the dynamic nature of protein expression.

Additionally, the majority of proteins undergo some form of posttranslational modification (PTM), further increasing proteomic complexity.

During the last 15 years, the broad scope of proteomics is only beginning to be realized due in large part to technological developments in mass spectrometry.

Originally developed almost 100 years ago to measure elemental atomic weights and the natural abundance of specific isotopes, MS was first used in the biological sciences to trace heavy isotopes through biological systems.

In later years, MS was used to sequence oligonucleotides and peptides and analyze nucleotide structure.

New isotopic tagging methods led to the quantitation of target proteins both in relative and absolute quantities.

All these technological advancements have resulted in methods that successfully analyze samples in solid, liquid or gas states.

The sensitivity of current mass spectrometers allows one to detect analytes at concentrations in the attomolar range (10 -18 ).

It also touches on sample preparation and liquid chromatographybased separation prior to MS analysis.

The nature of these components varies based on the purpose of the mass spectrometer, the type of data required, and the physical properties of the sample.

Samples are loaded into the mass spectrometer in liquid, gas or dried form and then vaporized and ionized by the ion source (e.g., APCI, DART, ESI).

The ions encounter electric andor magnetic fields from mass analyzers, which deflect the paths of individual ions based on their mz.

Commonly used mass analyzers include time-of-flight TOF, orbitraps, quadrupoles and ion traps, and each type has specific characteristics.

Mass analyzers can be used to separate all analytes in a sample for global analysis, or they can be used like a filter to deflect only specific ions towards the detector.

Most often, these detectors are electron multipliers or microchannel plates that emit a cascade of electrons when each ion hits the detector plate.

This cascade results in amplification of each ion hit for improved sensitivity.

This entire process is performed under an extreme vacuum (10 -6 to 10 -8 torr) to remove gas molecules and neutral and contaminating non-sample ions, which can collide with sample ions and alter their paths or produce non-specific reaction products.

Data analysis programs detect ions and organize them by their individual mz values and relative abundance.

These ions can then be identified via established databases that predict the identity of the molecule based on its mz value.

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