// 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: data\databaseTestQtof\DAIPENLPPLTADFAEDKDVCK_3_qtof.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: 2 | 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). Ions Per Residue: 6 | Number of ions per average residue. // 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): 15 | US shoe size. Default of 17. // Output -------------------------------------------------------------------------------- Number of sequences: 5 | Number of output sequences listed. A good bet is 5 Score threshold: 0.2 | Pr(c) is approximate probability that at least half of the sequence is correct. A good bet is 0.20.