9780521516358book.pdf

• NIST Chemistry WebBook. NIST is the National Institute for Standards and
  Technology. Data on specific compounds in the Chemistry WebBook can be searched by
  name, chemical formula, CAS (Chemical Abstracts Service) registry number, molecular
  mass or selected ion energetics and spectral properties. This site comprises electron
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9.7.2 Identification of proteins

Database searches to identify a particular protein that has been analysed by mass

spectrometry are particularly important. This section gives an overview of websites for

proteomic identification.

Identification of proteins can be carried out by using many websites, for example:

‘Mascot’ from Matrix Science (http://www.matrixscience.com/search_form_select.html)

and ‘Protein Prospector’ (http://prospector.ucsf.edu/). The search can be limited by

searching a particular species or taxon, e.g. mammalia only, thus increasing the speed.

However, when looking for a homologous sequence the species should not be defined.

The modification of cysteine residues, if any, should be included otherwise the number

of peptides matched to the theoretical list will be decreased, producing a worsehit.If no

cysteine modification has been carried out, and if the protein originates from a gel

sample, then much of this residue will have been converted to acrylamide-modified Cys.

Unmatched masses should be re-searched since sometimes two or more proteins

run together on electrophoresis. Note thedelta p.p.m.(the difference between the

a(4)

b*(4)

y*(3)

y(3)

a(8)++

y*(8)++

b*(5)

b(5), a(10)++

y(10)++

y(5)

y(9)++

b*(6)

b(6)

y(6)

b(8)

y(7)

b(9)

y(9)

Tandem MS region

Quantitation
of the four
samples

Reporter

groups

114–117

1000 200 300 400 500 600 700 800 900 1000

Fig. 9.28Identification and quantitation of proteins by iTRAQ reagents. During MS/MS (along with the usual

peptide fragmentation) the isobaric tag cleaves at the sites indicated. As result of fragmentation, there is neutral

loss of the balance group, and the reporter groups are generated, displaying diagnostic ions in the low-mass

region at betweenm/zvalues 114 to 117. Because this region is free of other common ions, quantification of the

peak areas of these resultant ions represents the relative amount of a given peptide in the respective sample.

395 9.7 Computing and database analysis