ProPAS: standalone software to analyze protein properties.

Abstract

Physicochemical properties of proteins/peptides are often used to separate proteins/peptides from complex biological samples in proteomics research, which is necessary for the further proteins/peptides identification. So, the analyses of these properties are very important for the design of proteomic experiments and the further analyses of identified results. Current available web-based tools are difficult to analyze large-scale datasets. Here we provide a standalone software ProPAS (Protein Properties Analyses Software) to calculate these properties in local computers. ProPAS could be used to calculate several physicochemical parameters of proteins/peptides, including the isoelectric point (pI), hydrophobicity (Hy) and mass weight (MW). Additionally, ProPAS provides the statistic results to get the number distribution along the parameter values. The results could be copied to other software such as Excel to get the distribution chart. The amino acid composition of all the input proteins/peptides could also be calculated from all input sequences. Detail description, updates and download link for ProPAS could be found at the website of http://bioinfo.hupo.org.cn/tools/ProPAS/propas.htm.

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Software


ProPAS: standalone software to analyze protein
properties


Songfeng Wu & Yunping Zhu*


State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, , 27 Taiping Road,
China; Beijing 100850, Yunping Zhu - Email: zhuyunping@gmail.com; Phone: 8610-80705225; *Corresponding author


Received December 29, 2011; Accepted January 07, 2012; Published February 03, 2012


Abstract:
Physicochemical properties of proteins/peptides are often used to separate proteins/peptides from complex biological samples in
proteomics research, which is necessary for the further proteins/peptides identification. So, the analyses of these properties are
very important for the design of proteomic experiments and the further analyses of identified results. Current available web-based
tools are difficult to analyze large-scale datasets. Here we provide a standalone software ProPAS (Protein Properties Analyses
Software) to calculate these properties in local computers. ProPAS could be used to calculate several physicochemical parameters
of proteins/peptides, including the isoelectric point (pI), hydrophobicity (Hy) and mass weight (MW). Additionally, ProPAS
provides the statistic results to get the number distribution along the parameter values. The results could be copied to other
software such as Excel to get the distribution chart. The amino acid composition of all the input proteins/peptides could also be
calculated from all input sequences. Detail description, updates and download link for ProPAS could be found at the website of
http://bioinfo.hupo.org.cn/tools/ProPAS/propas.htm.

ISSN 0973-2063 (online) 0973-8894 (print)
Bioinformation 8(3): 167-169 (2012)
 

167
© 2012 Biomedical Informatics

Background:
Protein identification is a basic task for proteomics research.
Usually, the proteins/peptides need to be separated according
to their physicochemical properties before the identification
[1]. The common used physicochemical properties include
isoelectric point, hydrophobicity and mass weight. So, the
calculation of these physicochemical properties is very
important and could be used for the design of proteomic
experiments. Further analyses of physicochemical properties
for the identified proteins might be helpful to discover the
experimental bias, which would be important for improving
the experiments. The analyses could also be used to discover
the different distribution caused by some biological factors,
for example the different isoelectric point and hydrophobicity
in different sub-cellular localization [2, 3]. Most current
available softwares for these physicochemical properties
calculation are web-based, including the software in ExPASy
[4]. The web-based softwares are difficult for the analyses of
large-scale datasets. ProPAS provide an alternative choice to
analyze the data in local computer, which could be used to
process small or large-scale datasets. Additionally, ProPAS
could also provide the statistic results to get the
protein/peptide
physicochemical properties.

Methodology:
Calculation of isoelectric point
Isoelectric point (pI) was estimated as the pH at which a
protein took on a neutral charge (R=0) [5]. (Please see
supplementary material for definition of R).

Calculation of hydrophobicity
Hydrophobicity value for each protein is calculated as the
mean value of hydrophobic index for all amino acids. In this
software, Kyte-Doolittle scale [6] is used as the hydrophobic
index. 

Calculation of mass weight
Protein mass weight (MW) is calculated by the addition of
average isotopic masses of amino acids in the protein and the
average isotopic mass of one water molecule. The mass
weight values for the amino acids are from ExPASy [7],
including 20 standard amino acids and 2 non-standard amino
acids (Selenocysteine and Pyrrolysine). Additionally, the
number distribution of these

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characters B (Asx: Aspartic acid or Asparagine), Z (Glx:
Glutamine or Glutamic acid) and X (Xaa: Any amino acid) are
also accepted for the calculation, whose mass values are
calculated as the mean values of the corresponding amino
acid masses weighted by their respective frequencies. In this
program, their mass values are: B (114.6686), Z (128.7531) and
X (111.1138).

Calculation of amino acid composition
Amino acid composition is calculated as the count and the
percentage for each amino acid from all the input
proteins/peptides. The software was developed by Perl script.
Figure 1 shows the interface and its functional modules of the
software.


Figure 1: The interface of ProPAS. The different functional
modules are showed in the interface: (1) input format options;
(2) text box for input data; (3) text box for input file and its
directory; (4) parameters that could be analyzed; (5) need
statistic or not; (6) range and step of the parameter for the
statistic; (7) file and directory that the results will be exported
to; (8) text box for output data; (9) button to calculate the
properties; (10) Button to save the results showed in text box
“8” to file; (11) Button to copy the results showed in text box
“8” to clipboard.

Input
The input data for the software includes
(a) One or more protein sequences with Fasta format (“Fasta”
in the software); (b) One protein/peptide with only amino
acid sequence (“Single plain sequence” in the software); (c)
One or more peptide sequences, one peptide for each line
(“Peptide list” in the software). The data could be input with
two different ways. Firstly, the data could be copied to the
clipboard and then pasted to the text box in the software.
Secondly, the data could be stored as a file and then the user
would find and select the file by clicking the “File open…”
button. If the data is provided by both of the above ways, only
the data from the file would be used for the calculation.
Parameter setting:
Sometimes, the user would only need to calculate some of the
parameters. It could be set in the parameter plate. De-select
any parameter would skip the calculation. For the distribution
statistic, the ranges and their steps could also be changed in
the parameter plate upon the requirement of the research.

Output:
The calculation results could be showed in the right text box
of the software, or be exported to the file if there is the file
name and its directory in the box following “Save to file:”
when running the program.

The output results include the following sections
(a) Result of the physicochemical properties for each
protein/peptide. It would list the values of pI, Hy and MW
for each protein. (b) Result of the pI statistic; (c) Result of the
MW statistic; (d) Result of the Hy statistic; (e) Result of the
amino acid composition statistic; in the statistic results, the
number and percent of each step of the parameters are
provided to get their distribution.

Caveat & future development:
The post-translational modifications are not considered in the
calculation, which would be added in the further
development. Some other parameters of protein properties
would also be considered if needed (for example, the protein
stability and so on).

Acknowledgment:
This work was supported by the Chinese National Key
Program of Basic
2011CB910601，2010CB912700).
Xiaofang Xue for the help of the software development.

References:
[1]
Ly L & Wasinger VC, Proteomics. 2011 11: 513 [PMID:
21241016].
[2]
Chan P & Warwicker J, BMC Biol. 2009 7: 69 [PMID:
19849832].
[3]
Zhang T et al. Comput Biol Chem. 2006 30: 367 [PMID:
16963318].
[4]
Wilkins MR et al. Methods Mol Biol. 1999 112: 531 [PMID:
10027275].
[5]
Bjellqvist B et al. Electrophoresis. 1993 14: 1023 [PMID:
8125050].
[6]
Kyte J & Doolittle RF, J Mol Biol. 1982 157: 105 [PMID:
7108955]
[7]
http://web.expasy.org/findmod/findmod_masses.html
#AA
[8]
Wu S et al. Proteomics. 2006 6: 449 [PMID: 16317776]

Research
We
(Grant
Ping
No.
Wan, thank
Edited by P Kangueane
Citation: Wu et al. Bioinformation 8(3): 167-169 (2012)
License statement: This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,
for non-commercial purposes, provided the original author and source are credited

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ISSN 0973-2063 (online) 0973-8894 (print)
Bioinformation 8(3):167-169 (2012)
 

169
© 2012 Biomedical Informatics
Supplementary material:

Methodology:
Calculation of isoelectric point
Isoelectric point (pI) was estimated as the pH at which a protein took on a neutral charge (R=0 in the following formula) [5]. For a
given sequence, the pI algorithm was as follows. In the formula, Naa represents the number of special amino acids in a special
protein, Kaa the values of pKR of special amino acids [8].

1
np
CRCRR
−=
2
His
ArgLys
p
KHKHKHKH
++++
][][][][
3
CT
TyrTyrCysCys
GluGlu
AspAsp
n
KHKHKHKHKH
+++++
][][][][][

?
(1)
(2)
NT
K
+
His
N
Arg Lys
H
HN
HNH
[
N
CR
+++=
+
+
+
+
+
+
+
+
][
][
][]

?
CT
Tyr CysGluAsp
KKN
KN
KN
CR
++++=
++++

?
(3)