Blazmass+ComPIL
Blazmass, a fast and sensitive proteomics search engine
ComPIL (Comprehensive Protein Identification Library), a set of peptide and protein databases for metaproteomics
See related Metaproteomics repository at Su Lab/metaproteomics
File formats
MS2 and SQT are plaintext file formats detailed in the following publication:
MS2 files can be generated from instrument RAW files using a tool such as RawExtractor or RawConverter
Input file format
Blazmass takes an MS2 file as input. MS2 files contain MS/MS precursor ion, charge, and fragment information:
MS2 Format
S 000040 000040 960.22797
I RetTime 0.25
I PrecursorInt 6606.3
I IonInjectionTime 150.000
I ActivationType HCD
I PrecursorFile MSMS_sample.ms1
I PrecursorScan 34
I InstrumentType FTMS
Z 4 3837.89004
109.4537 168.2 0
111.1992 175.5 0
112.6070 188.2 0
136.0749 575.7 0
143.1249 190.1 0
152.1059 178.3 0
...
Output file format
Blazmass outputs search results in the SQT file format, which contains unfiltered proteomic scoring information, including the best scoring peptide matches for each scan, parent proteins for each matched peptide, and other search-related information.
SQT Format
S 10210 [information for scan #10210]
M 1 [best scoring peptide match]
L [parent protein for peptide match 1]
L [parent protein for peptide match 1]
L [parent protein for peptide match 1]
M 2 [second-best scoring peptide match]
L [parent protein for peptide match 2]
L [parent protein for peptide match 2]
...
Running locally
tested on CentOS 6, RHEL 7, Linux Mint/Ubuntu 15.10
Requirements
- Java 1.7 (Oracle or OpenJDK)
- MongoDB 3.0+
- MongoDB databases can be running locally (
localhost
), remotely as a single node (typically using TCP port 27017), or sharded behind amongos
process (typically port 27018)
- MongoDB databases can be running locally (
- Databases
- see metaproteomics repository for build_compil
- or see here for demo databases
Instructions
- Download Blazmass+ComPIL
- Untar / extract using
tar -xvf blazmass_compil.tar.gz
- Modify parameters as desired in directory
example/blazmass.params
-- specifically, database connection information - Try a test search using
example/run.sh
Blazmass written by Robin Park, John Yates III, et al.
ComPIL/MongoDB integration by Sandip Chatterjee & Greg Stupp