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// Lutefisk parameters file
//
// If this file is present in the directory from which Lutefisk is invoked,
// then the value of the parameters listed in the 'VALUE' column below
// will override the program defaults.
//
// TITLE VALUE DEFAULT
CID Filename: Qtof_ELVISLIVESK.dta | CID Filename.
CID Quality: N | Check for CID data quality. (Y/N)
Peptide MW: 0 | Peptide molecular weight. Zero will calc. from input file.
Charge-state: 0 | Number of charges on the precursor ion. Zero will calc. from input file.
MaxEnt3: N | Data file processed using MaxEnt 3 (Qtof only) (Y/N)
// Mass Tolerances ----------------------------------------------------------------------
Peptide Error (u): 0.45 | Peptide molecular weight tolerance.
Fragment Error (u): 0.25 | Fragment ion tolerance. Must be 0.25 or less for qtof scoring to take effect.
Final Fragment Err (u): 0.04 | Fragment ion tolerance for final scoring of Qtof data. Zero will skip qtof scoring.
// Memory and Speed ---------------------------------------------------------------------
Max. Final Sequences: 20000 | Number of final sequences stored.
Max. Subsequences: 5000 | Number of subsequence allowed.
Mass Scrambles for Statistics: 0 | Number of times to use a wrong precursor mass (for calculating score significance).
// Spectral Processing ------------------------------------------------------------------
CID File Type: D | CID file type: D='.dta', F=ICIS text file, L=LCQ "text", T=tab text, N='.dat'
Profile/Centroid: C | Is this CID data in profile or centroid form? P=Profile, C=Centroid, A=Autodetect.
Peak Width (u): 0.75 | Peak width at about 10%. A value of 0 (zero) activates the auto-peak width mode.
Ion Threshold: 0.01 | Ion threshold. (Ions > average intensity x Ion threshold are utilized.)
Mass Offset (u): 0.0 | Mass offset.
Ions Per Window: 8 | Ions per input window (windows are 60 Da wide). 8 for Qtof, 6 for LCQ
Ions Per Residue: 6 | Number of ions per average residue. 6 for Qtof, 4 for LCQ
// Subsequencing ------------------------------------------------------------------------
Transition Mass (u): 5000 | Cutoff for monoisotopic to average mass calculations.
Fragmentation Pattern: Q | Fragmentation pattern (T=triple quad tryptic,L=ion trap tryptic, Q=Qtof tryptic)
Max. Gaps: -1 | Maximum number of gaps per subsequence. -1 implies a default value.
Extension Threshold: 0.15 | Extension threshold.
Max. Extensions: 6 | Maximum number of extensions per subsequence.
// Extras -------------------------------------------------------------------------------
Cysteine Mass: 160.03065 | Residue mass of cysteine. (160.03065, 161.01466, 208.06703 = carbamidomethyl, carboxymethyl and pyridylethyl)
Proteolysis: T | Type of proteolysis? T=tryptic, K=Lys-C, E=V8, D=AspN, and N=none of the above
Modified N-terminus: 1.0078 | N-terminal mass [1.0078(unmod), 43.0184(acetyl), 44.0136(carbamyl)]
Modified C-terminus: 17.0027 | C-terminal mass [17.0027(unmod), 16.0187(amide), 31.0184(methyl)]
Present Amino Acids: * | Amino acids known to be present in the peptide. * means none.
Absent Amino Acids: * | Amino acids known to be absent from the peptide. * means none.
Auto Tag: Y | Auto-tag (Y/N).
Tag Low Mass y Ion: 0 | Sequence tag - low mass y ion
Sequence Tag: * | Sequence tag - single letter code, no spaces, from low mass to high mass y ion
Tag High Mass y Ion: 0 | Sequence tag - high mass y ion
DB Sequence File: | File with sequences to score with the final results.
Shoe Size (US): 9.5 | US shoe size. Default of 17.
// Output --------------------------------------------------------------------------------
Number of sequences: 10 | Number of output sequences listed. A good bet is 10
Score threshold: 0.2 | Pr(c) is approximate probability that at least half of the sequence is correct. A good bet is 0.20.
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