Biomedical Engineering Reference
In-Depth Information
to the actual applications or documentation about them. Two
recent book publications cover the theory and application of the
software applications mentioned in the different sections of this
Bioinformatic software can be used to theoretically analyze a
proteome before even stepping into the laboratory, which can aid
in the design of an experiment. Once the LC-MS/MS data has
been acquired, it needs to be processed and converted into a peak
list before database searching and peptide and protein identifica-
tion. The LC-MS/MS data search results can be visualized and
compared before generating reports for use in the laboratory or
for publication. Recently, there has been a lot of focus on quan-
titation of proteins by MS/MS which requires specialized soft-
ware. There are a number of reasons why a large proportion of
the MS/MS spectra remain unidentified by a database search. A
second-pass search can be used to identify spectra of peptides with
unexpected post-translational modifications or that are a prod-
uct of non-specific enzyme cleavages. De novo sequencing can be
used to identify the peptides from some of the remaining spectra.
Once a list of all the proteins in a sample have been determined,
bioinformatics software can be used to query databases for biolog-
ical information about the proteins, their function, localization,
and known interaction partners. Information about LC-MS/MS
experiments, the data, and search results can be tracked, orga-
nized, and stored in Laboratory Information Management Sys-
tems (LIMS) and made available for data mining. Consideration
has to be made for the long-term storage of LC-MS/MS data
on computer servers. Raw data and search results may need to be
converted into standardized formats for data exchange and sub-
mittal to public repositories.
2. Theoretical
Analysis
of Proteomes
As the technologies used in experimental proteomics have multi-
plied, the need to model the effect of these technologies on the-
oretical analysis has grown. The choice of technologies used in
an experiment has an impact on the number of proteins that can
be identified. Proteomic experiments targeting specific proteins
will need careful choice of technologies to optimize the possibility
that the proteins of interest are present and identified. Theoretical
proteomic analysis provides a description of some aspects of the
proteome (for example, the proportion of the amino acids and
the molecular weight and p
I
of the proteins), which can be used
to design an experiment that targets proteins normally missed
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