
*******************************************************************************
--------------------------------- IADBs ------------------------------------
--------------------- Copyright © 2008-2015 Waters Corporation ---------------------
Version 2.175 Compiled: 11/19/2015 6:33 PM
Run at: 1/28/2023 10:22 PM
Command Line:

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs1108382046133725173.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs1108382046133725173.bin -proteinFASTAFileName C:\Users\Administrator\Downloads\NAO_REV_GALLUS_22.10.18_reverse.fas_def -outPutDirName C:\Users\Administrator\AppData\Local\Temp -outputUserDirName C:\Users\Administrator\AppData\Local\Temp -newWorkflowXML -maxCPUs 11 -WriteBinary 1

 Parameter XML file:
<IA_PARAMS>
    <FASTA_FORMAT VALUE="DEF" />
    <PRECURSOR_MHP_WINDOW_PPM VALUE="-1" />
    <PRODUCT_MHP_WINDOW_PPM VALUE="-1" />
    <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="600000" />
    <FALSE_POSITIVE_RATE VALUE="4" />
    <AQ_PROTEIN_ACCESSION VALUE="P00924" />
    <AQ_PROTEIN_MOLES VALUE="100" />
    <MANUAL_RESPONSE_FACTOR VALUE="-1" />
    <DIGESTS>
        <ANALYSIS_DIGESTOR MISSED_CLEAVAGES="1">
            <AMINO_ACID_SEQUENCE_DIGESTOR NAME="Trypsin" UUID="57e26a8c-2b26-43e8-98a9-b4dd34d76921">
                <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
*******************************************************************************
 Parameter XML file:       "C:\Users\Administrator\AppData\Local\Temp\plgs1108382046133725173.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs1108382046133725173.bin"
 Protein   FAS File:       "C:\Users\Administrator\Downloads\NAO_REV_GALLUS_22.10.18_reverse.fas_def"
 Output Directory:         "C:\Users\Administrator\AppData\Local\Temp"
 User Output Directory:    "C:\Users\Administrator\AppData\Local\Temp"

 Instrument Model:   XEVO-G2QTOF
 Instrument Serial#: YCA119
 Raw Input File: "G:\JOSE_SPOTS_DEZ22\22DEZ15_PLASMA_FRANGO_72.raw"
 Acquired Name: "22DEZ15_PLASMA_FRANGO_72"
 Acquired Date: "30-Dec-1899"
 Acquired Time: "00:00:00"
 Sample Description: "IBB"

Processed by:
 Apex3D version 3.0.14.11,  compiled: 6/18/2015 processed: 1/28/2023
    command line: "C:\PLGS3.0.3\lib\apex3d\Apex3D64.exe" -pRawDirName "G:\JOSE_SPOTS_DEZ22\22DEZ15_PLASMA_FRANGO_72.raw" -outputDirName "C:\Users\Administrator\AppData\Local\Temp" -lockmassZ2 785.8426 -lockMassToleranceAMU 0.4 -leThresholdCounts 500.0 -heThresholdCounts 50.0 -writeXML 1 -PLGS 1 

 Peptide3D version 2.120.5883.20180,  compiled: 2/9/2016 processed: 1/28/2023
    command line: C:\PLGS3.0.3\lib\apex3d\Peptide3D.exe -inputFilename C:\Users\Administrator\AppData\Local\Temp\22dez15_plasma_frango_72_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 19732.39
Precursor MHPlus Window PPM    = 5.067809 (set automatically by resolution)
Product MHPlus Window PPM      = 12.66952 (set automatically by resolution)
Max MHPlus Window PPM          = 25.33905
Bin FWHM Fraction              = 0.1428571
Report homologs                = True
Leucine Isoleucine homologs    = True
Min Amino Acids per PepFrag1   = 6
Min fragments per peptide      = 2
Min peptides per protein       = 1
Min fragments per protein      = 5
Max False positive rate        = 4
Pass 1 False positive rate     = 100
Max protein mass               = 600000
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
Allow Charge 1 only peptides   = True
Search Adducts                 = False
No Pass 2                      = False
No Pass 3                      = False
Non-specific Pass              = False

Read 707 LE ions, 14303 HE ions (14303 binned), 706 bins in 0.2774381 seconds
Read 115903 proteins in 5.0987665 seconds
Matched 181 out of 3829946 peptides in digest to 181 matches in 101 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 181 out of 3829946 peptides in digest to 181 matches in 101 of 115903 proteins
After Pass1:  7 distraction, 25 regular proteins
Curate calibration disabled : Only found 21 distraction peptides
Yellow-Green Threshold = 6 Red-Yellow Threshold = 5

Statistics:
pepBinomial: Min 0.0000 Max 0.0050 Mean 0.0011 StdDev 0.0022
precModelRT: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000
precMassErr: Min -2.3249 Max 0.9877 Mean -0.2933 StdDev 1.5270
fragSimilarity: Min 0.3746 Max 0.8320 Mean 0.6269 StdDev 0.1717
weightedSeqCoverage: Min 0.0882 Max 0.3333 Mean 0.1626 StdDev 0.1020
byTheoretical: Min -0.5737 Max -0.0703 Mean -0.2747 StdDev 0.2145
prodRtErr: Min 0.0000 Max 0.0181 Mean 0.0056 StdDev 0.0075
prodMassErr: Min 0.0000 Max 0.1141 Mean 0.0368 StdDev 0.0458

After Pass2 Depletion:  2 distraction, 7 regular proteins
After Filter Proteins:  0 distraction, 5 regular proteins

******************************* Results Summary ********************************

Number of hit groups:   	4
Proteins:
 Number of good matches:	5
                Green  :	4
                Yellow :	1
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	322
                Green  :	318
                Yellow :	4
                Red    :	0
Fragments:
 Number of matches:     	4,796
                                          Precursors 	 Products
 Number of PepFrag1 matches:                   195 	    3,488
     Green                                     192 	    3,475
     Yellow                                      3 	       13
     Red                                         0 	        0
 Number of PepFrag2 matches:                     9 	      200
     Green                                       9 	      200
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of MissedCleavage matches:              31 	      498
     Green                                      31 	      498
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of VarMod matches:                      39 	      446
     Green                                      39 	      446
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of InSource matches:                    38 	      126
     Green                                      37 	      125
     Yellow                                      1 	        1
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              8 	       27
     Green                                       8 	       27
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of NeutralLoss_NH3 matches:              2 	       11
     Green                                       2 	       11
     Yellow                                      0 	        0
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	5
                Green  :	4
                Yellow :	1
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	126
                Green  :	122
                Yellow :	4
                Red    :	0
Fragments:
 Number of matches:     	1,497
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    56 	      995
     Green                                      53 	      982
     Yellow                                      3 	       13
     Red                                         0 	        0
 Number of PepFrag2 matches:                     3 	       65
     Green                                       3 	       65
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of MissedCleavage matches:               9 	      152
     Green                                       9 	      152
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of VarMod matches:                      10 	      121
     Green                                      10 	      121
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of InSource matches:                    38 	      126
     Green                                      37 	      125
     Yellow                                      1 	        1
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              8 	       27
     Green                                       8 	       27
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of NeutralLoss_NH3 matches:              2 	       11
     Green                                       2 	       11
     Yellow                                      0 	        0
     Red                                         0 	        0
Total processing time: 10.9000477 seconds
