(New page: ==Project X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. This software has ...) |
|||
| Line 1: | Line 1: | ||
| - | ==Project | + | ==Project== |
X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. | X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. | ||
| Line 5: | Line 5: | ||
Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found [http://www.thegpm.org/docs/peptide_protein_expect.pdf here]. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used. | Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found [http://www.thegpm.org/docs/peptide_protein_expect.pdf here]. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used. | ||
| + | |||
| + | ==Latest release== | ||
| + | |||
| + | This release is the first of the new TORNADO versions of X! Tandem, which have the goal of utilizing available external annotation information it improve the performance of sequence identifications. The 2007.04.01 release started this project, by adding single nucleotide induce amino acid polymorphism annotation to searches. TORNADO introduces the capability of setting the potential modifications tested on a sequence by sequence basis, controlled by a BIOML annotation file. | ||
| + | System level changes | ||
| + | |||
| + | #A fix for the method to force the use of specific file formats (made by Patrick Lacasse) | ||
| + | #Addition of a class to handle sequence annotation files in BIOML format (saxmodhandler). | ||
| + | #Addition of a method to load the annotation file information into an STL map, in the class mprocess. | ||
| + | #When compiling on Linux platforms, several possible makefiles are provided. The default makefile will work for GCC version 4, with the expat libraries dynamically linked. The other makefiles are all in the src directory, with names like "Makefile_XXX" where XXX is a descriptive name indicating in which situations this file is appropriate. To use these files, use a command line like this: | ||
| + | |||
| + | >make -f Makefile_GCCv3 | ||
X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.
This software has a very simple, sophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output format is described here (PDF). This format is used for all of the X! series search engines, as well as the GPM and GPMDB.
Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.
This release is the first of the new TORNADO versions of X! Tandem, which have the goal of utilizing available external annotation information it improve the performance of sequence identifications. The 2007.04.01 release started this project, by adding single nucleotide induce amino acid polymorphism annotation to searches. TORNADO introduces the capability of setting the potential modifications tested on a sequence by sequence basis, controlled by a BIOML annotation file. System level changes
>make -f Makefile_GCCv3