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--------------------------------- IADBs ---------------------------------------
--------------------- Copyright © 2013 Waters Corporation ---------------------
Version 2.135.2.0 Compiled: 10/31/2013 1:59 PM
Run at: 1/18/2018 2:01 PM
Command Line:

-paraXMLFileName C:\Users\waters\AppData\Local\Temp\plgs646586056250535321.params -pep3DFilename C:\Users\waters\AppData\Local\Temp\plgs646586056250535321.xml -proteinFASTAFileName C:\PLGS3.0.2\demodbs\uniprot-reviewed_Euticotyledons.fasta_def -outPutDirName C:\Users\waters\AppData\Local\Temp -outputUserDirName C:\Users\waters\AppData\Local\Temp -newWorkflowXML -maxCPUs 11

 Parameter XML file:
<?xml version="1.0" encoding="UTF-8"?>
<IA_PARAMS>
    <FASTA_FORMAT VALUE="DEF"/>
    <PRECURSOR_MHP_WINDOW_PPM VALUE="50"/>
    <PRODUCT_MHP_WINDOW_PPM VALUE="100"/>
    <NUM_BY_MATCH_FOR_PEPTIDE_MINIMUM VALUE="2"/>
    <NUM_PEPTIDE_FOR_PROTEIN_MINIMUM VALUE="1"/>
    <NUM_BY_MATCH_FOR_PROTEIN_MINIMUM VALUE="5"/>
    <PROTEIN_MASS_MAXIMUM_AMU VALUE="250000"/>
    <FALSE_POSITIVE_RATE VALUE="100"/>
    <AQ_PROTEIN_ACCESSION VALUE=""/>
    <AQ_PROTEIN_MOLES VALUE="-1"/>
    <MANUAL_RESPONSE_FACTOR VALUE="-1"/>
    <DIGESTS>
        <ANALYSIS_DIGESTOR MISSED_CLEAVAGES="1">
            <AMINO_ACID_SEQUENCE_DIGESTOR NAME="Trypsin" UUID="7722d8bb-d02b-4479-b7ff-b12c2fe6d51f">
                <CLEAVES_AT AMINO_ACID="K" POSITION="C-TERM">
                    <EXCLUDES AMINO_ACID="P" POSITION="N-TERM"/>
                </CLEAVES_AT>
                <CLEAVES_AT AMINO_ACID="R" POSITION="C-TERM">
                    <EXCLUDES AMINO_ACID="P" POSITION="N-TERM"/>
                </CLEAVES_AT>
            </AMINO_ACID_SEQUENCE_DIGESTOR>
        </ANALYSIS_DIGESTOR>
    </DIGESTS>
    <MODIFICATIONS>
        <ANALYSIS_MODIFIER ENRICHED="FALSE" STATUS="FIXED">
            <MODIFIER MCAT_REAGENT="No" NAME="Carbamidomethyl+C">
                <MODIFIES APPLIES_TO="C" DELTA_MASS="57.0215" TYPE="SIDECHAIN"/>
            </MODIFIER>
        </ANALYSIS_MODIFIER>
        <ANALYSIS_MODIFIER ENRICHED="FALSE" STATUS="VARIABLE">
            <MODIFIER MCAT_REAGENT="No" NAME="Oxidation+M">
                <MODIFIES APPLIES_TO="M" DELTA_MASS="15.9949" TYPE="SIDECHAIN"/>
            </MODIFIER>
        </ANALYSIS_MODIFIER>
    </MODIFICATIONS>
</IA_PARAMS>


  Input parameters                                values
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 Parameter XML file:       "C:\Users\waters\AppData\Local\Temp\plgs646586056250535321.params"
 Spectrum  XML File:       "C:\Users\waters\AppData\Local\Temp\plgs646586056250535321.xml"
 Protein   FAS File:       "C:\PLGS3.0.2\demodbs\uniprot-reviewed_Euticotyledons.fasta_def"
 Output Directory:         "C:\Users\waters\AppData\Local\Temp"
 User Output Directory:    "C:\Users\waters\AppData\Local\Temp"

 Acquired Name: "02122017_CL_OU_Bindhu_1"
 Acquired Date: "02-Dec-2017"
 Acquired Time: "20:57:01"
 Sample Description: "02122017_CL_OU_Bindhu_1"

Resolution                  = 15235.15
Precursor MHPlus Window PPM = 50 (set by user)
Product MHPlus Window PPM   = 100 (set by user)
Max MHPlus Window PPM       = 200
Bin FWHM Fraction           = 0.1429
Report homologs             = True
Min fragments per peptide   = 2
Min peptides per protein    = 1
Min fragments per protein   = 5
Max False positive rate     = 100
Pass 1 False positive rate  = 100
Max protein mass            = 250000
Min ratio by to theoretical = 0.3
Min sumProdInten/precInten  = 0.03
Max sumProdInten/precInten  = 1
Max simultaneous varMods    = 3
Max CPUs                    = 11
ScoreFactors                = 1, 9, 3.5, 1, 1.9, 1, 2, 1
No Pass 2                   = False
No Pass 3                   = False
Non-specific Pass           = False

Read 127114 LE ions, 3018327 HE ions (1837961 binned), 107210 bins in 97.2460006 seconds
Read 53622 proteins in 2.4131045 seconds
Matched 1034406 out of 1551574 peptides in digest to 1034406 matches in 52397  of 53622 proteins
Insufficient pass 0 matches for mass cal
Matched 1034406 out of 1551574 peptides in digest to 1034406 matches in 52397  of 53622 proteins
After Pass1:  3982 distraction, 6006 regular proteins
Time to calc all pass2 raw pepScores 00:00:10.2992662

Calibrating AutoCurate Thresholds using 3829480 distraction peptides
Median Random pepScore 6.093177 Std Random pepScore 0.307318
Red-Yellow Threshold is 6.86 which is 2.50 stddevs above the mean
Yellow-Green Threshold is 7.32 which is 4.00 stddevs above the mean
Median Random raw pepScore 331.5 Std Random raw pepScore 314.5126
Time to run pass 2 depletion: 00:17:13.9972956
After Pass2 Depletion:  3055 distraction, 5106 regular proteins
After Filter Proteins:  0 distraction, 5106 regular proteins
Total processing time: 2036.4538606 seconds