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release_notes.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<title>X! tandem relase notes</title>
<style>
td {color: #444444;
font-weight: normal;
font-family: Verdana, Arial, Helvetica;
font-size: 10pt;}
li {color: #444444;
font-weight: normal;
font-family: Verdana, Arial, Helvetica;
font-size: 10pt;
padding-bottom: .5em;}
.td_b {color: black;
font-weight: bold;
font-family: Verdana, Arial, Helvetica;
font-size: 10pt;}
</style>
</head>
<body>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td width="600" align="left" valign="top" class="td_b">X! tandem release notes</td>
</tr>
<tr>
<td width="600" align="left" valign="top">X! tandem will be released periodically,
with the version numbering system formulated from the date of release. The
changes made to the system on each release are detailed in the list below.
Releases are listed with the most recent release on top.
<hr>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table5">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">Latest release: 2007.07.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release adds compatibility with 64 bit floating point
data in mzXML or mzData formats.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>An new override of the dtohl method in the saxhandler.cpp file
was added to deal with 64 bit floats.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table5">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2007.04.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release is the first version to support amino acid residue
polymorphism annotation. A file containing known coding mutations can be specified and the
search engine will check each specified version of those modified residues.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>Including SAPS required modification of the classes <i>mprocess</i> and
<i>mscore</i> as well as the addition of a new classs <i>mscoresap</i>, which
is specified in the mscorepam.h file. The new class follows the
same pattern as the other state machines for tracking sequence modifications. A class
that reads the XML-formatted SAPS annotation information has also
been added, <i>saxsaphandler</i>, which follows the same pattern as
the other BIOML processing classes.
</LI>
<LI>This version (and all subsequent ones) will use the preprocessor commands associated with
the compiler make processor to specify the platform being compiled. Previous
versions required the commenting out undesired options in the stdafx.h file. This
change includes the PLUGGABLE_SCORING preprocessor definition in mscore.h that
is necessary to alter the peptide scoring portion of the code.
</LI>
<LI>The Mac OSX version of the executable binaries is statically linked to
the most recent version of the XML parser expat. Unlike previous versions
it will not be necessary to have expat installed on the computer used
to run the search engine. The Linux/Unix builds are now the only
platforms onwhich dynamic linking is necessary.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table5">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2007.01.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release is the first release to support rho-diagrams
for the determination of expectation value thresholds. It also has a minor, but important
change to the interpretation of results to make the results of refinement rounds more
consistent. This release is also the first to support the Mac OS X 10.4 version for Intel
processors. Support for non-Intel processors will be discontinued as of the next release.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>The output file has a new output value in the "performance parameters" group,
for example:
<pre>
<group label="performance parameters" type="parameters">
<note label="quality values">117 34 22 10 5 2 1 0 0 1 0 1 0 0 0 0 0 0 0 0</note>
</group></pre>
This change was necessary to support the use of rho-diagrams in the GPM display software.
</LI>
<LI>The proteins reported as possible correct identifications have been changed somewhat.
In previous versions, it was possible for a protein to be reported as identified even if
it did not have any qualifying peptides that were found to have the specified enzymatic
cleavage: a protein could have peptides found only during the cleavage-at-every site round
or the point-mutation round. This behavior has been changed so that a protein must have
at least one significant peptide found to have the specified enzymatic cleavage.
</LI>
<LI>The implementation of point mutation detection has been altered so that if a particular
possible point mutation has been explained by any set of potential modifications, it will not
be included as a possible solution in the output.
</LI>
<li>The stdafx.h file has been altered to add in new preprocessor statements that
deal with the different versions of Mac OS X. These new statements are #OSX_TIGER
and #OSX_INTEL. To compile with OS X 10.4 on a PPC computer, uncomment both #OSX
and #OSX_TIGER. To compile with OS X 10.4 on an Intel computer, uncomment only
#OSX_INTEL.
</li>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table5">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2006.09.15</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release of X! Tandem/P3 contains several
minor changes to maintain cross-platform compatibility.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
Code that uses iterator math to determine the limits of a calculation
have been altered so that the iterators are not incremented passed the
end of an STL container. Incrementing iterators passed the end of a
container generates a run-time error when compiled with Microsoft Visual
C++ 2005. The precompiler variable _CRT_SECURE_NO_DEPRECATE has been
defined for the Visual C++ compiler, to prevent the generation of
unnecessary compiler warnings for the use of C string functions, such as "strcpy".
</LI>
<LI>
The SAXTandemInputHandler::characters method has been updated to
improve its performance and to handle escape characters correctly (suggested by Brendan Maclean).
</LI>
<LI>
The documentation and precompiler defines in stdafx.h that provide cross-platform compatibility
for 64-bit integer types have been updated.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2006.06.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release of X! Tandem contains two
fixes to improve compatibility with Linux and one adjustment to be compatible
with X! Hunter.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
On at least some Linux platforms, astersiks (*) in FASTA file were not being
processed properly. This has been corrected by Brendan Maclean.
</LI>
<LI>
Some mzXML files could produce memory problems, when combined with some
spectrum processing parameters because a vector was not being cleared between
processing individual spectra. This problem did not affect the results of the
search, but it could cause memory paging when using a large file.
</LI>
<LI>
The taxonomy xml file has always contained <i>type</i> specification, which was
not used by X! Tandem. Now X! Tandem enforces that FASTA or FASTA.PRO files
must be specificed with <i>type="peptide"</i>.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2006.04.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top"><p>This release of X! Tandem includes a
number of additions to the system API. These changes are mainly for
programmers, allowing for greater customization of searches. Some of these
features have been present in previous versions of X! Tandem, but have been
either undocumented or unsufficiently well tested.</p>
<p>This version of the X! Tandem code also merges the code for X! P3. The P3
executable can be compiled by uncommenting the preprocessor variable X_P3 in
"stdafx.h". Adding in the P3 code was done by creating several
classes that are extensions of the normal Tandem classes and using a small
number of preprocessor directives. These new classes have the prefix <b>p3</b>.</p>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top">Added parameters:
<ol>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/olp.html">output, log path</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/om.html">output, message</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/oosc.html">output, one sequence copy</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/osp.html">output, sequence path</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/refmm.html">refine, modification mass</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/rsp.html">refine, sequence path</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/rtp.html">refine, tic percent</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/scp.html">scoring, cyclic permuation</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/sir.html">scoring, include reverse</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/spsbs.html">spectrum, sequence batch size</a>
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2006.04.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top"><p>This release of X! Tandem includes a
number of additions to the system API. These changes are mainly for
programmers, allowing for greater customization of searches. Some of these
features have been present in previous versions of X! Tandem, but have been
either undocumented or unsufficiently well tested.</p>
<p>This version of the X! Tandem code also merges the code for X! P3. The P3
executable can be compiled by uncommenting the preprocessor variable X_P3 in
"stdafx.h". Adding in the P3 code was done by creating several
classes that are extensions of the normal Tandem classes and using a small
number of preprocessor directives. These new classes have the prefix <b>p3</b>.</p>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top">Added parameters:
<ol>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/olp.html">output, log path</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/om.html">output, message</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/oosc.html">output, one sequence copy</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/osp.html">output, sequence path</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/refmm.html">refine, modification mass</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/rsp.html">refine, sequence path</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/rtp.html">refine, tic percent</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/scp.html">scoring, cyclic permutation</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/sir.html">scoring, include reverse</a>
</LI>
<LI>
<a href="http://www.thegpm.org/TANDEM/api/spsbs.html">spectrum, sequence batch size</a>
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2006.02.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release of X! Tandem contains
several small fixes in response to error reports.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
The C-ion mass calculation has been improved for electron-capture ion source
identifications, suggested by David Fenyo.
</LI>
<LI>
A problem relating to an include file that caused compilation difficulties for
some versions of GCC on some version of Linux has been fixed.
</LI>
<li>
The calculation of parent ion mass difference has been improved, to provide
better consistency for very accurate (< 1 ppm) parent ion mass
determinations.
</li>
<li>
The "semi" cleavage state machine has been adjusted for better
performance.
</li>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2005.12.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release of X! Tandem adds several
new features, as well as improving the XML standards compatibility of the
system.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
An improved handling of hex encoded binary information in mzXML and mzData
files, for 64-bit processors, added by Steven Wiley.
</LI>
<LI>
Addition of testing for N-terminal glutamic acid cyclization, suggested by Oleg
Krohkin.
</LI>
<li>
Addition of "semi" enzymatic cleavage (specific enzyme cleavage at
one end of a peptide and non-specific cleavage at the other), suggested by Matt
Monroe.
</li>
<li>
An improved system for detecting XML file types, suggested by Steven Wiley.
</li>
<li>
Support for variant methods of expressing parent ion charge in mzData v. 1.05,
added by Fredrik Levander.
</li>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2005.10.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release of X! Tandem adds several
new features, as well as improving on some of the existing features. It
contains a number of engineering architectural changes meant to allow simpler
access to some of the key algorithms in the system.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
An improved version of the state machine that lists all of the possible
potential modification states of a peptide sequence was written by Brendan
Maclean. This version is both more thorough and faster than the previous code.
</LI>
<LI>
The capability of using chemical average masses for fragment ion mass
calculations was added by Brendan Maclean.
</LI>
<li>
A simplification of the mprocess class that allows for a "pluggin"
approach to adding new refinement modules was designed and implemented by Rob
Craig.
</li>
<li>
An improved routine for correcting for isotope peaks and multiple observations
of similar masses was made by Patrick Lacasse.
</li>
<li>
An additional state machine using cyclic peptide sequence permutation to
compensate for small sequence collections and for large mass peptides was
added. This feature is based on a suggestions made separately by Tom Blackwell
& David States and Patrick Lacasse.</li>
<li>
An improved sorting method to improve the consistency of homologous sequence
assignments was added by Rob Craig.
</li>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2005.08.15</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">The changes in this release are aimed at
increasing XML compliance and high accuracy mass calculation consistency.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
The handlers for GAML spectra, taxonomy files and input parameter files have to
changed to using expat, rather than custom routines.
</LI>
<LI>
A more flexible mass calculation class has been added to improve molecular mass
consistency for high accuracy calculations.
</LI>
<li>
The input spectrum file type detection method has been improved by adding the
possibility of forcing it to select one file type. This forcing is done using
the input parameter "spectrum, path type" parameters, which can have
the values: dta, pkl, mgf, gaml, mzxml or mzdata. If this parameter is missing
or of zero length, the normal file type detection scheme is used.
</li>
</ol>
</td>
</tr>
<tr>
<td class="td_b" bgcolor="#dd6622"><span class="top_label">2005.06.01</span></td>
</tr>
<tr>
<td width="600" align="left" valign="top">This version corrects an issue that could
arise in large MudPIT data sets with large numbers of redundant
identifications. The calculation of the protein expectation value in previous
versions was susceptible to floating point overflows when making this
calculation, resulting in unpredictable values.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2005.03.21</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release adds the ability to process <a href="http://sashimi.sourceforge.net/software_glossolalia.html">
mzxml</a> and <a href="http://psidev.sourceforge.net/ms/#mzdata">mzdata</a>
file formats using <a href="http://expat.sourceforge.net/">eXpat</a> library of
functions. Most of the changes in this release were initially made by Patrick
Lacasse (Université Laval, Dept. of Medicine, supported by Genome Québec) with
the final version and optimizations made by Brendan MacLean, from the Fred
Hutchinson Cancer Research Center. Also, the ability to define the amino acid
residue masses has been added allowing users to change the default masses when
doing N15 experiments for example.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
New classes have been added to allow the processing of mzxml and mzdata file
formats.<br />
Two of the new classes are publicly derived from loadspectrum, a custom class
specific to Tandem. Two others are publicly derived from the xml parser class
SAXSpectraHandler which is imported from the expat library of functions. The
xml parser classes use the expat functions exclusively to parse the input in
order to load it into the traditional Tandem spectra data members.
</LI>
<LI>
base64.cpp and base64.h have been added to allow b64_decode_mio() function
calls, which are needed to decode the spectra in mzxml and mzdata spectra
files.
</LI>
<LI>
Included in the src folder is the libexpat.lib which is required to compile new
versions of the executable on Windows. Linux and OSX machines should have the
required libraries as part of the core operating system.
</LI>
<LI>
A new function has been added to msequtilites that allows amino acid residue
masses to be defined by an xml input file. If the parameter 'protein, modified
residue mass file' is defined in the input.xml, the masses are taken from the
file defined by that parameter. An example of the format can be viewed <a href="http://human.thegpm.org/tandem/methods/n15.xml">
here</a>.
</LI>
</ol>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2005.02.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release contains modifications
necessary to insert new types of peptide scoring systems as well as to deal
effectively with high accuracy parent ion measurements, which are now available
in some types of mass spectrometers. Most of the changes in this release were
made by Brendan MacLean, from the Fred Hutchinson Cancer Research Center.
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
Several new classes have been added, to make the scoring system
"pluggable", i.e., it is now much easier to alter the scoring system
used, for the purposes of bioinformatics investigations. These changes are
mainly of interest to informatics professionals and they should not affect the
normal operation of the software for users.
</LI>
<LI>
The calculation of parent ion mass has been changed, taking more care as to the
mass of added groups and correctly accounting for electron masses.
</LI>
<LI>
Better statistical methods have been added to deal with the small number of
possible peptides generated from a list of protein sequences that have a very
high accurately determined parent ion mass.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.11.15.3</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release adds in several features
that were originally scheduled to appear in the 2004.11.15 release, but which
were pushed back from the initial release. The 2004.11.15.2 version was not
generally released.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
Spectra that are interpreted as being caused by a prompt neutral loss now have
the prompt loss specified in the appropriate <aa> node in the output.
</LI>
<LI>
Correction of an issue with the OS X version that resulted in improper reading
of ".pro" sequence files. Initially, the ".pro" format was
to have both little endian and big endian versions, however this became too
confusing to maintain. The current plan is to only use the little endian format
and to compensate for this on-the-fly in the OS X version.
</LI>
<LI>
The maximum parent ion charge to be used can now be specified using the
"spectrum, maximum parent charge" parameter. This parameter has a
default value of 4. This change was made necessary because of high charge
states being called by some MS peak assignment software, which caused spurious
assignments.
</LI>
<LI>
The first round of refinement (finding partially cleaved peptides) has been
extended, so that it possible to repeat it with different sets of modifications
and motifs. These additional refinement rounds are specified by adding
parameters using the following format:
<ul>
<li>
Round 1: "refine, potential modification mass"<br>
"refine, potential modification motif"
</li>
<li>
Round 2: "refine, potential modification mass 1"<br>
"refine, potential modification motif 1"
</li>
<li>
Round 3: "refine, potential modification mass 2"<br>
"refine, potential modification motif 2"
</li>
</ul>
This will continue until both of the next pair of parameters are either missing
or neither contain an ampersand (@).
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.11.15</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This is a maintenance release, to correct
one issue identified in the 2004.09.01 release.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
An error that resulted in the incorrect interpretation of some motifs was
corrected.
</LI>
<LI>
Addition of spectrum prefiltering to remove repeated spectra from the initial
set of mass spectra. This feature compares spectra using a dot product
calculation and removes spectra that have vector representations that point in
the same direction. The most intense spectrum out of a set of repeated spectra
is kept and used for analysis. This type of filtering can remove up to 90% of
spectra from a MudPit-style run, making data analysis and interpretation
easier.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.09.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This is a maintenance release, to correct
one issue identified in the 2004.08.01 release.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
A possible floating-point overrun error that could lead to 0.0 expectation
values for high scoring peptides was detected from GPMDB submissions has been
corrected.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.08.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This is a maintenance release, to correct
several issues identified in the 2004.07.15 release.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
An error that reduced the score for triply-charged ions was corrected.
</LI>
<LI>
Quantitation information was added to the output XML file.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table4">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.07.15</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This is a major release of TANDEM,
sufficiently different from previous releases to merit a major revision number:
this release will be referred to as TANDEM 2.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
The memory management throughout the program has been analyzed and altered to
minimize the amount of memory used per spectrum. This effort has reduced the
amount of memory used in single threaded operation by as much as 60%: the
improvement for double threaded operation may be as much as 80%.
</LI>
<LI>
The threading model has been changed to allow for the use of multiple
processeors in the refinement process. TANDEM 1 separated work between the
threads by dividing up the sequences to search, so that each thread would only
search a subset of the sequences in a FASTA file. TANDEM 2 divides up the mass
spectra between threads, so that each thread searches a subset of the mass
spectra. This change makes it easier to divide up the refinement job, but means
that running more than one thread on a single processor will degrade the
performance of the software. For best performance, it is now important to keep
the number of threads and the number of processors the same.
</LI>
<LI>
The refinement process has been improved in accuracy by applying a logical
filter after each step of refinement. This means that once a refinement step is
completed, the new results obtained from the refinement are examined and it the
new results are not significantly better than those obtained from a simpler
search, they are discarded and the simpler results retained. This filtering
significantly reduces the complexity of analyzing results when there may be a
variety of similar modification patterns or point mutations that explain a
particular spectrum.
</LI>
<LI>
Validation of results using reversed sequence databases has been built-in to
the search process. This validation may be turned on or off, using the new
input parameter "<i>scoring, include reverse</i>" (values = yes|no).
This validation process tabulates the number of unique high probability hits
from the reversed sequence search and places them in the output file, along
with estimates of the false positive rate based on TANDEM's stochastic
histogramming technique and the estimate derived from the reversed sequence
process. NOTE: When this validation method is used, twice as many sequences
must be processed (both forward and reversed), which may require significantly
more processing time.
</LI>
<LI>
Numerous small optimizations have been made, particularly for loading and
reporting the results for very large collections of mass spectra.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table4">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.06.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release adds three new
functionalities to X! TANDEM. These new functions make it possible to modify
protein sequences in new ways.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
The ability to specify modifications based on sequence motifs was added to both
the normal search and refinement steps. A comma separated list of motifs in
slightly modified PROSITE format can be used to only modify specific residues.
An example of this format is:<BR>
204@[N!]{P}[ST]{P} - which says a motif that has an N, followed by any residue
except P, followed by an S or a T, followed by any residue except P is
specified. Modify the residue in the group containing the exclamation point (in
this case the N) by adding 204 Da.
<BR>
The peptides containing this motif are checked both with and without this
modification, so it is interpreted the same way that a "potential" modification
is interpretted. The rules for creating these motifs are:
<ul>
<li>
Square brackets "[]" indicate any of the residues contained is
possible;</li>
<li>
French brackets "{}" indicate that any of the residues contained is
forbidden;</li>
<li>
A bare letter is interpreted as if it was in square brackets and can be
modified with an exclamation point, e.g. 16@[M!] is the same as 16M!;</li>
<li>
An exclamation point indicates the position of modification;</li>
<li>
The letter "X" indicates any residue;</li>
and
<li>
Round brackets "()" indicate a count, e.g. "X(10)" means
ten X's in a row;</li>
<li>
All other characters are ignored, e.g. 80@[ST!]PX[KR] is the same as
80@[ST!]-P-X-[KR].</li>
</ul>
</LI>
<LI>
The ability to specify prompt neutral losses for potential modifications
(including motifs) has been added. This neutral loss is specified by adding a
colon followed by the mass corresponding to the loss. For example:<BR>
80@S specified phosporylation without loss, while 80:-98@S specifies the
neutral loss of the phosphate group.
</LI>
<LI>
The ability to specify on a sequence by sequence level specific fixed
modifications of residues by the residue number has been added. This capability
cannot be exploited currently because of a lack of sequence lists that contain
this type of information. However, an appropriately translated version of a
database such as SWISSPROT could be used to provide this information.
</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table4">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.05.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release is a maintenance release. It
should improve memory usage for very long sequence lists, but other wise should
be neutral.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
The mechanism for storing sequences in the mprocess class has been changed.
Previously, a copy of each protein sequence was stored with each peptide model
associated with a spectrum. Now, a master list of protein sequences is kept and
only a lookup number is stored with each peptide model. This change improves
memory management for very large pools of redundant proteins or very long lists
of spectra.</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table4">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.04.10</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release corrects an interpretation
problem introduced in the 2004.04.01 release. This problem results in an
overemphasis on peptides found in the refinement steps.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
The refinement processing was returned to its previous state, so that only the
best scoring peptides from the refinement process are reported.</LI>
</ol>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table4">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.04.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release is the result of an effort
to reduce memory usage by TANDEM. This effort has resulted in a 70% reduction
in memory usage, when using large data files.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
GAML spectra, such as those in output xml files, can now be used as input data.</LI>
<LI>
The length of scoring histogram arrays have been altered to improve memory
usage.
</LI>
<LI>
Several instances of temporary copies of data have been removed and other data
structures cleared as soon as possible after use.</LI>
</ol>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">Corrected problems</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
A behavior that resulted in the lost of the last character in sequences in some
FASTA files has been corrected.</LI>
<LI>
A compatibility issue resulting from various choices for the size of the size_t
STL variable on unix platforms has been corrected, so that most unix platforms
should compile without modifying the linux version of the code.</LI>
</ol>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">Known problems</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
No problems known at time of release</LI>
</ol>
<hr>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table4">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.03.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release fixes a number of
compatibility issues and unexpected behaviors in Tandem and associated
formating files.</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
A new state machine was added to perform N- and C- terminal partial
modifications. Previous versions used these modifications as complete
modifications only.</LI>
<LI>
The optimization for the minimum number of residues considered was removed and
replaced with the constant value of 4. The prior optimization did not produce a
significant improvement in speed, but it did cause occasional problems with
large neutral losses.</LI>
<LI>
The xslt and css files have been updated to conform more closely to
specification, making them compatible with the FireFox browser.</LI>
</ol>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">Corrected problems</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
A behavior that allowed the occasional consideration of peptides with too many
missed cleavage sites was fixed.</LI>
<LI>
A compatibility issue for starting threads on some unix platforms has been
corrected, so that most unix platforms should compile without modifying the
linux version of the code.</LI>
</ol>
</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">Known problems</td>
</tr>
<tr>
<td width="600" align="left" valign="top"><ol>
<LI>
No problems known at time of release</LI>
</ol>
<hr>
</td>
</tr>
</table>
<table border="0" cellpadding="3" cellspacing="3" ID="Table3">
<tr>
<td width="600" align="left" valign="top" class="td_b" bgcolor="#dd6622">2004.02.01</td>
</tr>
<tr>
<td width="600" align="left" valign="top">This release introduces the capability of
detecting point mutations in protein sequences</td>
</tr>
<tr>
<td width="600" align="left" valign="top" class="td_b">System level changes</td>