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

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs6287636818068074502.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs6287636818068074502.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\plgs6287636818068074502.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs6287636818068074502.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_68.raw"
 Acquired Name: "22DEZ15_PLASMA_FRANGO_68"
 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_68.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_68_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 19998
Precursor MHPlus Window PPM    = 5.000499 (set automatically by resolution)
Product MHPlus Window PPM      = 12.50125 (set automatically by resolution)
Max MHPlus Window PPM          = 25.00249
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 184 LE ions, 2879 HE ions (2879 binned), 182 bins in 0.1072352 seconds
Read 115903 proteins in 4.8209432 seconds
Matched 40 out of 3829946 peptides in digest to 40 matches in 6 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 40 out of 3829946 peptides in digest to 40 matches in 6 of 115903 proteins
After Pass1:  0 distraction, 7 regular proteins
Curate calibration disabled : Only found 0 distraction peptides
Yellow-Green Threshold = 6 Red-Yellow Threshold = 5

Statistics:
pepBinomial: none
precModelRT: none
precMassErr: none
fragSimilarity: none
weightedSeqCoverage: none
byTheoretical: none
prodRtErr: none
prodMassErr: none

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

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

Number of hit groups:   	4
Proteins:
 Number of good matches:	7
                Green  :	7
                Yellow :	0
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	78
                Green  :	55
                Yellow :	23
                Red    :	0
Fragments:
 Number of matches:     	577
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    62 	      483
     Green                                      43 	      395
     Yellow                                     19 	       88
     Red                                         0 	        0
 Number of MissedCleavage matches:               5 	       34
     Green                                       4 	       28
     Yellow                                      1 	        6
     Red                                         0 	        0
 Number of VarMod matches:                       9 	       55
     Green                                       7 	       47
     Yellow                                      2 	        8
     Red                                         0 	        0
 Number of InSource matches:                     2 	        5
     Green                                       1 	        2
     Yellow                                      1 	        3
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	4
                Green  :	4
                Yellow :	0
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	57
                Green  :	39
                Yellow :	18
                Red    :	0
Fragments:
 Number of matches:     	406
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    44 	      335
     Green                                      30 	      265
     Yellow                                     14 	       70
     Red                                         0 	        0
 Number of MissedCleavage matches:               4 	       25
     Green                                       3 	       19
     Yellow                                      1 	        6
     Red                                         0 	        0
 Number of VarMod matches:                       7 	       41
     Green                                       5 	       33
     Yellow                                      2 	        8
     Red                                         0 	        0
 Number of InSource matches:                     2 	        5
     Green                                       1 	        2
     Yellow                                      1 	        3
     Red                                         0 	        0
Total processing time: 9.7469321 seconds
