# Proteomics/Emerging and Miscellaneous Proteomics Technologies

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# Emerging and Miscellaneous Technologies in Proteomics

This part of the book will be an area where proteomics techniques that
have been newly developed will be discussed. Techniques that do not
currently fit into any other part of the book can also be added to this
page. As chapters or sections are added elsewhere that discuss these
techniques in the context of a greater proteomics problem, the
information on this page will be moved to those pages.

## X-Ray Tomography

**Description and Discussion of X-ray Tomography.**

A new branch of X-ray microscopy is being used in proteomics analysis.
This is called X-ray Tomography. This method uses projected images to
calculate and reconstruct a 3D object. This technology is being used in
proteomics to determine the location of labeled proteins or large
complexes within a cell. This technique can also be used in conjunction
with images of cells from light based microscopes to help identify where
a protein is located and how this location factors in to its function
and identification.

## Introduction to Proteoinformatics

Proteoinformatics is the use of bioinformatics and computational biology
techniques solely within the realm of protein identification and
proteomics. Proteoinformatics is currently in its infancy and the
largest work being done is on standardizing databases and data
submission. Other proteoinformatic work is being done on the image
analysis of 2D gels and other images in proteomics used to help identify
and annotate proteins in the proteome.

### Protein Identification Database

#### What are Protein Identification Databases?

Protein Identifications Databases such as ProFound at Rockefeller
University and Protein Prospector at the UCSF Mass Spectrometry Facility
are used to help identify proteins found with proteomics techniques such
as mass spectrometry. Digestion of proteins into peptide fragments
allows each protein to break apart in a different way, resulting in a
unique peptide fingerprint that can be used to identify the protein. The
masses of these fragments as well as the molecular weights and
isoelectric points are what is stored in many of these databases. This
data can be used to perform high-throughput protein identification.

#### The Future of Protein Identification Databases

In order to continue advancing the cause of mapping the human proteome,
international databases need to be established which integrate both
transcriptome and proteome data. The Human Proteome Organization is
currently working on establishing a defined standard for data submission
and annotation for the many different proteomics techniques currently
used to identify and annotate proteins.

### New Techniques in Image Analysis

According to the Image Analysis Wikipedia page, \"Image analysis is the
extraction of meaningful information from images.\" In terms of
Proteomics, image analysis can be used to compare different images
generated using proteomics techniques, such as 2D-PAGE gel images. New
programs are being developed that will help to optomize and automate the
process of locating a protein spot between two gel images in order to
identify the differences between 2D-PAGE gels. Other programs can be
used to help clean up and remove variability between these images as
well.

## Laser Capture Microdissection

!Diagram of Laser Capture
Microdissection
Laser capture microdissection or LCM is a process that isolates and
removes distinct populations from a tissue. This will facilitate the
comparison of diseased tissue with normal tissue from an organism.

In LCM, an infrared laser beam melts a thermosensitive polymer film that
traps a specific group of cells. This polymer film is then extracted and
moved to a test tube where an extraction buffer is used to remove the
groups of cells for more advanced proteomics analysis such as 2D-PAGE,
Ion Chromatography, etc. This technology will become more useful as
systems with higher sensitivity for analysis of smaller amounts of
tissue become developed and realized.

## Proteomic Complex Detection using Sedimentation

Approaches such as TAP tagging, which require the addition of fusion
proteins, can interfere with protein interactions that would have
normally occurred. Many times it takes a great deal of work to express
these tagged proteins, so this technique is used to give evidence that
there is a stable protein complex detected early on in the proteomics
experiment before more laborious approaches are used to isolate and
identify the protein complexes of interest. Issues also occur in MS and
2D Gel processes where one cannot be sure that a portion of a gel spot
is the desired protein because multiple proteins could be traveling
together in that spot as a complex.

This is where proteomic complex detection using sedimentation (ProCoDeS)
is applicable. ProCoDeS is a technique for the high-throughput
identification of both soluble and membrane proteins that are found in
stable complexes. Relative sizes of protein complexes are estimated via
their sedimentation in a gradient. In this case a rate zonal gradient or
RZG is used to better estimate the relative size of protein complexes.
The distribution of a protein of interest in this sedimentation can be
detected using classic techniques such as Western Blotting or newer
techniques such as ICAT. This can be done for a large number of
proteins. Thus, ProCoDeS can be used to identify stable protein
complexes. ProCoDeS is especially well suited for the screening of
unrefined cellular material to help find new proteins that cannot be
discovered because they exist in protein complexes such as proteins
found in protein membranes.

Next Chapter: Protein Identification - Mass
Spectrometry

## References

1.  Hartman, N. T., et al. \"Proteomic Complex Detection Using
    Sedimentation\"
    Anal. Chem., 79, 5, 2078 - 2083, 2007.
2.  NCT Proteomics Group \"Emerging
    Technologies\"
    National Institutes of Environmental Health Sciences
3.  NCT Proteomics Group
    \"ProteoInformatics\"
    National Institutes of Environmental Health Sciences
4.  \"Wikipedia: Image
    Analysis
5.  \"Wikipedia: Proteomics
6.  \"Wikipedia: X-ray
    Tomography

