SLM Transform Beta (Comet)

Welcome to the SLM-Transform (beta) wiki!

This wiki contains detailed information on how to use SLM-Index Beta.

Important

This is the beta implementation of SLM-Index and does not contain full features. The purpose of this implementation is to demonstrate the integratability of SLM-Index as well as to benchmark SLM-Index memory footprint and query speed.

What do you need?

1. make
2. cmake
3. libdivsufsort
4. Windows: MinGW

Install libdivsufsort

1. Get libdivsufsort from here: https://github.com/y-256/libdivsufsort
2. libdivsufsort can be configured to use OpenMP by modifying CMakeLists.txt.
3. Follow the instructions to install the libdivsufsort.

Linux

Assuming /lds is the path to libdivsufsort home,

1. Navigate to /lds/build/lib/CMakeFiles/divsufsort.dir
2. Execute the command: ar rcs libdivsufsort.a
3. Copy the libdivsufsort.a to /slmindexbeta/CometSearch/libdivsufsort
4. Also copy the divsufsort.h, config.h and lfs.h from the installed directory to /slmindexbeta/CometSearch/libdivsufsort

Windows

You will need Eclipse C/C++ IDE and MinGW GCC/G++ to build a SLM-Transform compatible libdivsufsort.

1. open Windows Powershell
2. Navigate to /lds and execute mkdir build and then cd build
3. Navigate to /lds and execute cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="../../" -G "Eclipse CDT4 - MinGW Makefiles" ..
4. Open Eclipse, right click anywhere in the "Project Explorer" and "Import".
5. Put the path to /lds/build and import the project.
6. Right click on the project and build the project.
7. Copy the built lib/libdivsufsort.dll.a and paste as /slmindexbeta/CometSearch/libdivsufsort/Windows/libdivsufsort.a
8. Also copy the include/lfs.h, config.h and divsufsort.h to /slmindexbeta/CometSearch/libdivsufsort/Windows

How to build SLM-Transform Beta

1. Open the Cygwin shell or Git Bash shell.
2. Navigate to SLM-Transform home directory
3. Execute the following command: make -j<JOBS>
4. Note that in above command, you can skip the -j <JOBS> if working with Linux.

How to Run samples

1. Unzip the /slmindexbeta/samples/rat.tar.gz -> ratNew2cleavages.fasta
2. Traverse to /slmindexbeta>/output/bin directory and execute: cp ../../samples/comet.params ./
3. Run: ./comet.exe ../../samples/*.ms2
4. The results (PIN and PEPXML) files will be placed in /samples directory

How to search MS/MS data against SLM-Index

1. Digest the proteome database using Protein Digestion Simulator or OpenMS.
2. Remove the redundant peptide sequences in the digested database using DBToolkit.
3. Optional: The decoy database can be generated and appended to the target database using DBToolkit

Edit the comet.params file

1. Add the path to the database file.
2. Configure the number and types of modifications that should be added to SLM-Index Beta.
3. Configure the digestion parameters for SLM-Index to validate the sequences in the database file.
4. Configure the result and output format.
5. Configure the capacity of modified peptides that could be added to SLM-Index Beta.

Note:

1. If capacity is smaller than the number of modified peptides generated from the normal peptides, SLM-Index Beta will exit and throw a error message for the user to either increase the capacity or reduce the number/types of modifications to be added.
2. If the set capacity is greater than the spectra/peptides in the index, the extra memory will automatically be released while construction of index.
3. The max fragment charge: 3
4. Max digestion mass: 65kDa
5. The num_threads paramter controls the number of threads that can be used for indexing. The querying is restricted to 1 core.
6. The key-value sort for SLM Ion Index construction is handled by libdivsufsort. Please enable OpenMP when building libdivsufsort to enable parallel sort operation.