Sipros3

Sipros is a database-searching algorithm for peptide and protein identification in shotgun proteomics.

Key applications:

1. Regular database searching

2. Stable isotope probing

3. Identification of post-translational modifications

4. Identification of amino acid mutations.

Unique features:

1. Scalable to high-performance computing

2. Full integration with ProRata for quantification

Installation

Windows

Double click

Sipros-ProRata_V3.0_Setup.exe

Linux

tar -zxzf Sipros-ProRata_V3.0_Linux.tar.gz

cd Sipros-ProRata_V3.0_Linux/src

if Sipros will be used on a desktop, you just need Openmp feature. Please execute

make

You will get binary file Sipros_openmp

If you need the MPI/OpenMP feature of Sipros, please execute

make -f MPIMakefile

You will get binary file Sipros_openmp_mpi

In this readme, we will use Sipros to refer to the binary file. Please note that the current makefile uses g++ by default. If you want to switch to other compilers or add flags, please update the corresponding makefile.

Usage

Configuration file setup

Configure file setting

# is for comments.

[] is used for section name, e.g., [Section Name].

= is used for assigning features, e.g., Search_Type = Regular

{} is used for specifying key value, e.g., PTM{!} = NQR

Currently, there are 35 symbols available for specifying ptms, which are

~ ! @ $ % ^ & * ( ) _ + ` – | \ : ” ; ‘ < > ? . /

1 2 3 4 5 6 7 8 9 0

Please don’t use these reserved symbols: { } # [ ] = ,

Neutral loss can be specified by PTM{1to2}, e.g., PTM{>to|} = ST. If symbol2 is nothing, it can be specified by PTM{1to}, e.g., PTM{>to} = ST.

Regular searches

1. Create configure file

   Please refer to http://code.google.com/p/sipros/wiki/ConfigureFileSetting for technical details. An example is available athttp://code.google.com/p/sipros/source/browse/trunk/Sipros3.0/Sipros-src/SiprosConfigRegular.cfg

2. FT1 and FT2 files

   Please refer to http://code.google.com/p/raxport/ for generating FT1 and FT2 files

3. Pre-processing

The current version of scripts has been tested using Python 2.7.2, so if you are using different versions of Python (2.6.X or 3.X), you are encouraged to try with Python 2.7.2. If you want to use reverseseq.py, Biopython is required.

cd Sipros-ProRata_V3.0_Linux/scripts

Generate reverse sequence

python reverseseq.py -i original_database_file -o output_database_file

The step will generate a new database file with reverse sequences.

4. Run Sipros

   The easiest way for running Sipros is

   ./Sipros -c configurefilename -w workingdirectory

   Sipros will use all .FT2 files in the working directory. Results (.sip files) will be saved on working directory by default. You can specify output directory by specifying -o. If you just want to specify one FT2 file, you can use -f like,

   ./Sipros -c configurefilename -f FT2filename If you want to slice screen output, please add -s. In Sipros_openmp_mpi, you are allowing to specify -g like

   ./Sipros -g configurefiledirectory -w workingdirectory if you have many configure files.

   Please note that you can get help information by flag -h.

5. Post-processing

   The current version of scripts has been tested using Python 2.7.2, so if you are using different versions of Python (2.6.X or 3.X), you are encouraged to try with Python 2.7.2.

   cd Sipros-ProRata_V3.0_Linux/scripts

6. Peptide filtering

   python sipros_peptides_filtering.py -c configurefile -w workingdirectory

   All sip files, output files of Sipros, should be in the working directory. The step will generate related psm.txt and pep.txt

7. Peptide assembling

   python sipros_peptides_assembling.py -c configurefile -w workingdirectory

   The psm.txt and pep.txt files generated by the filtering step will be used in this step. And the step will generate pro.txt, pro2pep.txt, and pro2psm.txt files.

Post-translational Modification

Pro2ptm (Biopython needs to be installed)

python pro2ptm.py -c configurefile -w workingdirectory

Script pro2ptm.py will generate pro2ptm.txt file

If you also need pro2ptm.prorata.txt file, please run pro2ptm.py first and add ProRata_LabelFree_Peptide.txt, a output file of ProRata, to the working directory. Then run

python prorata_pro2ptm.py -w workingdirectory

This step will generate pro2ptm.prorata.txt file.

Stable isotope probing

python ClusterSip.py -c configurefile -w workingdirectory

This step will generate pro.cluster.txt and pro2psm.cluster.txt files.

Isobaric chemical labeling

python isobaric.py -c configurefile -w workingdirectory

python pro2isobaric.py -c configurefile -w workingdirectory

This step will generate pro.isobaric.txt, psm.isobaric.txt, and pro2psm.isobaric.txt files.