X! Search Engine Development
 X! Tandem FAQ See also: The GPM faq 1. Where are the results created? The results are written to the bin folder. If you are running linux make sure that the permissions on this folder allow for new files to be created. 2. What does the taxonomy.xml file do? This file is used as a taxon-to-file matching list. The URL paths in this file must point to the location of your local fasta files. To add a new taxonomy, follow the existing format of this file. Each taxonomy can contain one or more URL as in the example below.   To use this new taxonomy in your search, edit the input.xml file as follows.  yeast  3. What does the input.xml file do? Each one of the parameters for X! Tandem is entered as a labeled note node. Any of the entries in the default_input.xml file can be over-ridden by adding a corresponding entry to this file. This file represents a minimum input file, with only entries for the default settings, the output file and the input spectra file name. 4. What does the default_input.xml file do? This file contains labeled note nodes which carry the input parameters to tandem. For more information, look at the notes and descriptions in this file. 5. What is fasta_pro.exe used for? fasta_pro.exe is a supplementary program which enables users to create optimized files from fasta files. It is run from the command line as follows:  \path\to\tandem\fasta>fasta_pro nr-Saccharomyces-cerevisiae.fasta  This will create a file called nr-Saccharomyces-cerevisiae.fasta.pro in the same directory. Make sure to add the .pro extension to the path(s) in taxonomy.xml if you convert the files this way. 6.What types of data files can I use? X! Tandem is set up to use DTA, PKL or MGF files. These formats are ASCII files that are generated by a mass spectrometer's data handling system. This is an example of a pkl file that contains the values from more than one spectrum. 415.4407 347.4898 3 52.8570 1.1043 57.8380 1.1043 64.9675 1.1043 70.0623 1.1043 .... .... .... 401.7685 318.7188 3 49.9661 1.1043 55.6181 1.1043 73.7716 1.1043 76.2013 1.1043 98.4095 1.1043 .... .... ....  The first line has 3 values, each separated by a space. The first value (415.4407 and 401.7685) is the parent ion mass/charge ratio. The next value (347.4898 and 318.7188) is the parent ion intensity. The last value (3 and 3) is the parent ion charge. Each line after, this until there is a blank line, contains 2 values. Again they are separated by a space. The value pairs are the daughter ion masses and daughter ion intensities. This is an example of a dta file that contains the values from more than one spectrum. 929.278 2 104.997 2 114.036 2 133.052 2 151.593 2 .... .... .... 1003.2 2 108.084 2 123.007 2 126.249 4 142.525 4 .... .... ....  The first line has 2 values, separated by a space. The first value (929.278 and 1003.2) is the parent ion M+H. The next value (2 and 2) is the parent ion charge. Each line after, this until there is a blank line, contains 2 values. Again they are separated by a space. The value pairs are the daughter ion masses and daughter ion intensities. This is an example of an MGF file that contains the values from more than one spectrum. BEGIN IONS PEPMASS=820.998855732003 CHARGE=1+ TITLE=Elution from: 0.14 to 0.14 period: 0 experiment: 2 cycles: 1 200.9942 2.3857 354.9856 2.3857 370.9314 5.1571 388.9714 9.6857 390.9608 2.7429 END IONS BEGIN IONS PEPMASS=691.910270874147 CHARGE=2+ TITLE=Elution from: 0.03 to 0.03 period: 0 experiment: 1 cycles: 1 264.8982 30.0286 264.9944 8.9429 435.8989 3.2857 442.9097 4.2571 478.9086 3.6571 END IONS  Each spectra is contained within a set of BEGIN IONS and END IONS tags. The value following PEPMASS= is the parent ion mass/charge ratio. The value following CHARGE= is the parent ion charge. The lines after the TITLE entry are pairs of daughter ion masses and intensities separated by a space. 7. Can tandem provide dual modifications like an ICAT experiment? Tandem will allow two modifications on the same residue like in an ICAT experiment. The following is taken from the API description of the residue, modification mass parameter: If a residue labelling strategy is being used where there are two types of reagents for modifying a residue (e.g., C), one with mass L1 and the other with mass L2, the following method can be used to find both types of labelled peptide in the same analysis. Add the value L1@C to the residue, modification mass parameter Add the value (L2-L1)@C to the residue, potential modification mass parameter Because potential and complete modifications are treated separately internally by TANDEM, this will result in finding peptides modified with both types of parameters. 8. I get the error: 'ld: can't locate file for: -lexpat' when compiling on OSX It looks like the linker isn't finding the expat libs. Try adding the path to the expat lib files on the LDFLAGS line of the Makefile: LDFLAGS = -lpthread -L/usr/lib -L/path/to/libs -lm -lexpat