<?xml version=“1.0”?> <?xml-stylesheet type=“text/xsl” href=“tandem-input-style.xsl”?> <bioml>

<note>spectrum parameters</note>

<note type="input" label="spectrum, parent monoisotopic mass error minus">2.0</note>
<note type="input" label="spectrum, parent monoisotopic mass error plus">4.0</note>
        <note>PRECURSOR MASS TOLERANCE. This is monoisotopic mass, so for non-accurate-mass instruments, for which the precursor is often taken nearer to the isotopically averaged mass, an asymmetric tolerance (-2.0 Da to 4.0 Da) is preferable. This somewhat imitates a (-3.0 Da to 3.0 Da) window for averaged mass (but not exactly).</note>
<note type="input" label="spectrum, parent monoisotopic mass isotope error">no</note>
<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
        <note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
<note type="input" label="spectrum, parent monoisotopic mass error units">Daltons</note>
        <note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
        <note>This parameter has no effect in k-score scoring.</note>
<note type="input" label="spectrum, fragment mass type">monoisotopic</note>
        <note>values are monoisotopic|average </note>

<note>spectrum conditioning parameters</note>

<note type="input" label="spectrum, use conditioning">no</note>
        <note>For k-score scoring, it is recommended spectrum conditioning be turned OFF for best performance. All of the spectrum filtering and preprocessing options below in this section will be inactive.</note>
<note type="input" label="spectrum, dynamic range">10000.0</note>
<note type="input" label="spectrum, total peaks">400</note> 
<note type="input" label="spectrum, maximum parent charge">5</note>
<note type="input" label="spectrum, use noise suppression">yes</note>
<note type="input" label="spectrum, minimum parent m+h">600.0</note>
<note type="input" label="spectrum, minimum fragment mz">125.0</note>
<note type="input" label="spectrum, minimum peaks">10</note> 
<note type="input" label="spectrum, threads">1</note>
<note type="input" label="spectrum, sequence batch size">1000</note>

<note>residue modification parameters</note>

<note type="input" label="residue, modification mass"></note>
        <note>STATIC MODIFICATION. The format of this parameter is m@X, where m is the modfication mass in Daltons and X is the appropriate residue to modify. Lists of modifications are separated by commas. For example, to modify M and C with the addition of 16.0 Daltons, the parameter line would be +16.0@M,+16.0@C. Positive and negative values are allowed.</note>
<note type="input" label="residue, potential modification mass"></note>
        <note>VARIABLE MODIFICATION. The format of this parameter is the same as the format for residue, modification mass (see above).</note>
<note type="input" label="residue, potential modification motif"></note>
        <note>VARIABLE MODIFICATION IN A MOTIF. The format of this parameter is similar to residue, modification mass, with the addition of a modified PROSITE notation sequence motif specification. For example, a value of 80@[ST!]PX[KR] indicates a modification of either S or T when followed by P, and residue and the a K or an R. A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it is NOT followed by a P, then either an S or a T, NOT followed by a P. Positive and negative values are allowed. </note>

<note>protein parameters</note>

<note type="input" label="protein, taxon">no default</note>
        <note>SEQUENCE DATABASE TO SEARCH. This refers to identifiers in taxonomy.xml.</note>
<note type="input" label="protein, cleavage site">[RK]|{P}</note>
        <note>ENZYME SPECIFICITY. This setting corresponds to the enzyme trypsin. The first characters in brackets represent residues N-terminal to the bond - the '|' pipe - and the second set of characters represent residues C-terminal to the bond. The characters must be in square brackets (denoting that only these residues are allowed for a cleavage) or french brackets (denoting that these residues cannot be in that position). Use UPPERCASE characters. To denote cleavage at any residue, use [X]|[X] and reset the scoring, maximum missed cleavage site parameter (see below) to something like 50. </note>
<note type="input" label="protein, modified residue mass file"></note>
<note type="input" label="protein, N-terminal residue modification mass"></note>
<note type="input" label="protein, C-terminal residue modification mass"></note>
<note type="input" label="protein, homolog management">no</note>
        <note>if yes, an upper limit is set on the number of homologues kept for a particular spectrum</note>

<note>model refinement parameters</note>

<note type="input" label="refine">no</note>
<note type="input" label="refine, modification mass"></note>
<note type="input" label="refine, sequence path"></note>
<note type="input" label="refine, tic percent">10</note>
<note type="input" label="refine, spectrum synthesis">yes</note>
<note type="input" label="refine, maximum valid expectation value">0.1</note>
<note type="input" label="refine, potential N-terminus modifications"></note>
<note type="input" label="refine, potential C-terminus modifications"></note>
<note type="input" label="refine, unanticipated cleavage">no</note>
<note type="input" label="refine, potential modification mass"></note>
<note type="input" label="refine, point mutations">no</note>
<note type="input" label="refine, use potential modifications for full refinement">no</note>
<note type="input" label="refine, point mutations">no</note>
<note type="input" label="refine, potential modification motif"></note>

<note>scoring parameters</note>

<note type="input" label="scoring, algorithm">k-score</note>
<note type="input" label="scoring, minimum ion count">1</note>
<note type="input" label="scoring, maximum missed cleavage sites">2</note>
<note type="input" label="scoring, x ions">no</note>
<note type="input" label="scoring, y ions">yes</note>
<note type="input" label="scoring, z ions">no</note>
<note type="input" label="scoring, a ions">no</note>
<note type="input" label="scoring, b ions">yes</note>
<note type="input" label="scoring, c ions">no</note>
<note type="input" label="scoring, cyclic permutation">no</note>
        <note>if yes, cyclic peptide sequence permutation is used to pad the scoring histograms</note>
<note type="input" label="scoring, include reverse">no</note>
        <note>if yes, then reversed sequences are searched at the same time as forward sequences</note>
<note type="input" label="scoring, cyclic permutation">no</note>
<note type="input" label="scoring, include reverse">no</note>

<note>output parameters</note>

<note type="input" label="output, log path"></note>
<note type="input" label="output, message">1234567890</note>
<note type="input" label="output, sequence path"></note>
<note type="input" label="output, path">output.xml</note>
<note type="input" label="output, sort results by">spectrum</note>
        <note>values = protein|spectrum (spectrum is the default)</note>
<note type="input" label="output, path hashing">no</note>
        <note>values = yes|no</note>
<note type="input" label="output, xsl path">tandem-style.xsl</note>
<note type="input" label="output, parameters">yes</note>
        <note>values = yes|no</note>
<note type="input" label="output, performance">yes</note>
        <note>values = yes|no</note>
<note type="input" label="output, spectra">no</note>
        <note>values = yes|no</note>
<note type="input" label="output, histograms">no</note>
        <note>values = yes|no</note>
<note type="input" label="output, proteins">yes</note>
        <note>values = yes|no</note>
<note type="input" label="output, sequences">no</note>
        <note>values = yes|no</note>
<note type="input" label="output, one sequence copy">no</note>
        <note>values = yes|no, set to yes to produce only one copy of each protein sequence in the output xml</note>
<note type="input" label="output, results">all</note>
        <note>values = all|valid|stochastic</note>
<note type="input" label="output, maximum valid expectation value">0.1</note>
        <note>value is used in the valid|stochastic setting of output, results</note>
<note type="input" label="output, histogram column width">30</note>
        <note>values any integer greater than 0. Setting this to '1' makes cutting and pasting histograms into spread sheet programs easier.</note>

<note type=“description”>ADDITIONAL EXPLANATIONS</note>

<note type="description">Each one of the parameters for X! tandem is entered as a labeled note node. In the current version of X!, keep those note nodes on a single line.</note>
<note type="description">The presence of the type 'input' is necessary if a note is to be considered an input parameter. </note>
<note type="description">Any of the parameters that are paths to files may require alteration for a particular installation. Full path names usually cause the least trouble, but there is no reason not to use relative path names, if that is the most convenient.</note>
<note type="description">Any parameter values set in the 'list path, default parameters' file are reset by entries in the normal input file, if they are present. Otherwise, the default set is used. </note>
<note type="description">The 'list path, taxonomy information' file must exist.</note>
<note type="description">The directory containing the 'output, path' file must exist: it will not be created.</note>
<note type="description">The 'output, xsl path' is optional: it is only of use if a good XSLT style sheet exists.</note>

</bioml>