MS-Align+Tag

For running MS-Align+Tag on sample dataset unpack MsAlignTag.zip. Also you need Java 6 or higher installed.

On Windows execute the command line

java -server -Xmx4G -cp log4j-1.2.15.jar;MsAlignConsole-0.7.1.7284.jar;tagFinder.jar ru.spbau.bioinf.tagfinder.Tag4Finder

On Unix/Linux/Mac execute the command line

java -server -Xmx4G -cp log4j-1.2.15.jar:MsAlignConsole-0.7.1.7284.jar:tagFinder.jar ru.spbau.bioinf.tagfinder.Tag4Finder

If you want to run the algorithm on another dataset add the path to the data directory as a parameter. This directory should contain one *.fasta file with the protein database and one *.msalign with scans data generated by MS-Deconv.

The ouput looks like

=================================================================================================

candidatesCount = 20
batchSize = 20
peptideLength = 150
Initializing indexes...
#Total number of scans for process: 2018
#Started at Wed Mar 07 13:00:13 GMT+04:00 2012
502
503
504
506
507
508
510 2748 844.6923567647009 1 gi|16766157|ref|NP_461772.1| hydrogenase 3 membrane subunit [Salmonella typhimurium LT2]
511
512
514 3299 1.879564586115111E-13 1 gi|16766708|ref|NP_462323.1| 50S ribosomal subunit protein X [Salmonella typhimurium LT2]
515 3299 5.705388055234657E-8 5 gi|16766708|ref|NP_462323.1| 50S ribosomal subunit protein X [Salmonella typhimurium LT2]
516 3299 7.995884739732998E-12 2 gi|16766708|ref|NP_462323.1| 50S ribosomal subunit protein X [Salmonella typhimurium LT2]
518 1364 114.05170092851007 1 gi|16764759|ref|NP_460374.1| needle complex inner membrane lipoprotein [Salmonella typhimurium LT2]

scanId is the SCANS value from *.msalign file, proteinId is the index of the corresponding entry in *.fasta file ( the indices start from 0), E-value is calculated by MsAlignConsole-0.7.1.7284.jar.

We ignore scans representing spectra with less than 10 peaks and/or precursor mass less than 2500 Da.