Biology Reference
In-Depth Information
Independent of the quantitative method adopted (labeling or
label-free) the protein inference problem is an issue that deserves
attention. It is a consequence of the existence of shared, degener-
ate, or redundant peptides (i.e., when the sequence of an identified
peptide is present in more than one protein entry) [
26
]. When pro-
tein identification is performed using “unique peptides only”, it is
clear which peptides map to which protein. However, some pro-
teins have high identity at the primary sequence level, turning data
analysis into a complex and challenging task [
1
]. After detection of
the shared peptides, they may be ignored and the MS/MS spectra
associated to them will be counted multiple times (1), excluded
from data analysis which may result in underrepresentation of the
quantitative value observed for the proteins sharing peptides (2), or
distributed across the protein entries (3).
2
Materials
Noncommercial software and tools with user-friendly interface
(Fig.
2
):
1. Mspire-sequest
0.2.1/frames
) [
27
].
2. Search Engine Processor (
http://proteomics.iocruz.br/
Softwares.aspx
) [
28
].
3. Regrouper (
http://proteomics.iocruz.br/Softwares.aspx
).
4. PatternLab (
http://proteomics.iocruz.br/Softwares.aspx
) [
29
].
5. MUsite (
http://musite.sourceforge.net/
) [
30
].
6. Blast2GO (
http://www.blast2go.com/b2glaunch
) [
31
].
7. Permutmatrix (
http://www.lirmm.fr/~caraux/PermutMatrix/
)
[
32
].
3
Methods
The executable that reads and supports the conversion from
Bioworks Sequest Results File (SRF) to SQT files was developed by
Prof. John T. Prince in Ruby programming language. The con-
verter will work on any platform. The original publication [
27
] and
complete documentation of this program can be found at
http://
3.1 Generation
of SQT Files
1. Download Ruby Installer for Windows from
http://rubyinstaller.
