*******************************************************************************
--------------------------------- IADBs ---------------------------------------
--------------------- Copyright © 2013 Waters Corporation ---------------------
Version 2.135.2.0 Compiled: 10/31/2013 1:59 PM
Run at: 4/13/2018 11:30 AM
Command Line:

-paraXMLFileName C:\Users\waters\AppData\Local\Temp\plgs4600503467983072195.params -pep3DFilename C:\Users\waters\AppData\Local\Temp\plgs4600503467983072195.bin -proteinFASTAFileName C:\PLGS3.0.2\demodbs\uniprot-reviewed_viridiplantae.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="0a017806-3674-44be-affa-1413ee6f81fb">
                <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\plgs4600503467983072195.params"
 Spectrum  Bin File:       "C:\Users\waters\AppData\Local\Temp\plgs4600503467983072195.bin"
 Protein   FAS File:       "C:\PLGS3.0.2\demodbs\uniprot-reviewed_viridiplantae.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_2.raw"
 Acquired Name: "02122017_TL_OU_Bindhu_2"
 Acquired Date: "30-Dec-1899"
 Acquired Time: "00:00:00"
 Sample Description: "02122017_TL_OU_Bindhu_2"

Processed by:
 Apex3D version 2.128.9.0,  compiled: 9/19/2013 processed: 4/13/2018
    command line: C:\PLGS3.0.2\bin\..\lib\apex3d\Apex3D64.exe -pRawDirName D:\Data\2017\December\OU_Bindhu\02122017_TL_OU_Bindhu_2.raw -outputDirName C:\Users\waters\AppData\Local\Temp -outputUserDirName C:\Users\waters\AppData\Local\Temp -lockmassZ2 785.8426 -lockMassToleranceAMU 0.5 -leThresholdCounts 135.0 -heThresholdCounts 20.0 -binIntenThreshold 1000 -writeXML 1 -PLGS 1 

 Peptide3D version 2.96.5010.13362,  compiled: 9/19/2013 processed: 4/13/2018
    command line: C:\PLGS3.0.2\lib\apex3d\Peptide3D.exe -inputFilename C:\Users\waters\AppData\Local\Temp\02122017_tl_ou_bindhu_2_Apex3D.bin -outputDirName C:\Users\waters\AppData\Local\Temp -outputUserDirName C:\Users\waters\AppData\Local\Temp -minLEMHPlus 350.0


Resolution                  = 13012.59
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 124650 LE ions, 1581694 HE ions (1581694 binned), 72166 bins in 30.6556854 seconds
Read 78822 proteins in 3.3541839 seconds
Matched 1236602 out of 2186819 peptides in digest to 1236602 matches in 76198  of 78822 proteins
Insufficient pass 0 matches for mass cal
Matched 1236602 out of 2186819 peptides in digest to 1236602 matches in 76198  of 78822 proteins
After Pass1:  3060 distraction, 5691 regular proteins
Time to calc all pass2 raw pepScores 00:00:04.7674813

Calibrating AutoCurate Thresholds using 1879851 distraction peptides
Median Random pepScore 5.732989 Std Random pepScore 0.3070295
Red-Yellow Threshold is 6.50 which is 2.50 stddevs above the mean
Yellow-Green Threshold is 6.96 which is 4.00 stddevs above the mean
Median Random raw pepScore 283.5411 Std Random raw pepScore 258.5953
Time to run pass 2 depletion: 00:05:55.1545634
After Pass2 Depletion:  2029 distraction, 4614 regular proteins
After Filter Proteins:  0 distraction, 4614 regular proteins
Total processing time: 1126.8886367 seconds