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--------------------------------- IADBs ---------------------------------------
--------------------- Copyright © 2013 Waters Corporation ---------------------
Version 2.135.2.0 Compiled: 10/31/2013 1:59 PM
Run at: 1/19/2018 10:24 AM
Command Line:

-paraXMLFileName C:\Users\waters\AppData\Local\Temp\plgs9042081980214833176.params -pep3DFilename C:\Users\waters\AppData\Local\Temp\plgs9042081980214833176.bin -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\plgs9042081980214833176.params"
 Spectrum  Bin File:       "C:\Users\waters\AppData\Local\Temp\plgs9042081980214833176.bin"
 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"

 Instrument Model:   SYNAPT-G2
 Instrument Serial#: NotSet
 Raw Input File: "D:\Data\2017\December\OU_Bindhu\02122017_TL_OU_Bindhu_1.raw"
 Acquired Name: "02122017_TL_OU_Bindhu_1"
 Acquired Date: "30-Dec-1899"
 Acquired Time: "00:00:00"
 Sample Description: "02122017_TL_OU_Bindhu_1"

Processed by:
 Apex3D version 2.128.9.0,  compiled: 9/19/2013 processed: 1/18/2018
    command line: C:\PLGS3.0.2\bin\..\lib\apex3d\Apex3D64.exe -pRawDirName D:\Data\2017\December\OU_Bindhu\02122017_TL_OU_Bindhu_1.raw -outputDirName C:\Users\waters\AppData\Local\Temp -outputUserDirName C:\Users\waters\AppData\Local\Temp -lockmassZ2 785.8426 -lockMassToleranceAMU 0.25 -leThresholdCounts 150.0 -heThresholdCounts 10.0 -binIntenThreshold 500 -writeXML 1 -PLGS 1 

 Peptide3D version 2.96.5010.13362,  compiled: 9/19/2013 processed: 1/18/2018
    command line: C:\PLGS3.0.2\lib\apex3d\Peptide3D.exe -inputFilename C:\Users\waters\AppData\Local\Temp\02122017_tl_ou_bindhu_1_Apex3D.bin -outputDirName C:\Users\waters\AppData\Local\Temp -outputUserDirName C:\Users\waters\AppData\Local\Temp -minLEMHPlus 350.0


Resolution                  = 13526.85
Precursor MHPlus Window PPM = 50 (set by user)
Product MHPlus Window PPM   = 100 (set by user)
Max MHPlus Window PPM       = 200
Bin FWHM Fraction           = 0.1428571
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 125155 LE ions, 2858580 HE ions (2858580 binned), 106362 bins in 55.315019 seconds
Read 53622 proteins in 5.1412629 seconds
Matched 1015432 out of 1551574 peptides in digest to 1015432 matches in 52407  of 53622 proteins
Insufficient pass 0 matches for mass cal
Matched 1015432 out of 1551574 peptides in digest to 1015432 matches in 52407  of 53622 proteins
After Pass1:  4039 distraction, 6235 regular proteins
Time to calc all pass2 raw pepScores 00:00:16.9606221

Calibrating AutoCurate Thresholds using 3610637 distraction peptides
Median Random pepScore 5.962633 Std Random pepScore 0.3071017
Red-Yellow Threshold is 6.73 which is 2.50 stddevs above the mean
Yellow-Green Threshold is 7.19 which is 4.00 stddevs above the mean
Median Random raw pepScore 295.1569 Std Random raw pepScore 274.1426
Time to run pass 2 depletion: 00:15:20.3139769
After Pass2 Depletion:  2932 distraction, 5266 regular proteins
After Filter Proteins:  0 distraction, 5266 regular proteins
Total processing time: 1905.7003186 seconds