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

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs2603007459303025970.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs2603007459303025970.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\plgs2603007459303025970.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs2603007459303025970.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_79.raw"
 Acquired Name: "22DEZ15_PLASMA_FRANGO_79"
 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_79.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_79_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 19675.75
Precursor MHPlus Window PPM    = 5.082398 (set automatically by resolution)
Product MHPlus Window PPM      = 12.70599 (set automatically by resolution)
Max MHPlus Window PPM          = 25.41199
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 55 LE ions, 1218 HE ions (1218 binned), 54 bins in 0.080689 seconds
Read 115903 proteins in 4.6925914 seconds
Matched 2 out of 3829946 peptides in digest to 2 matches in 2 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 2 out of 3829946 peptides in digest to 2 matches in 2 of 115903 proteins
After Pass1:  0 distraction, 2 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, 2 regular proteins
After Filter Proteins:  0 distraction, 2 regular proteins

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

Number of hit groups:   	1
Proteins:
 Number of good matches:	2
                Green  :	2
                Yellow :	0
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	5
                Green  :	5
                Yellow :	0
                Red    :	0
Fragments:
 Number of matches:     	60
                                          Precursors 	 Products
 Number of PepFrag1 matches:                     3 	       26
     Green                                       3 	       26
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of VarMod matches:                       2 	       34
     Green                                       2 	       34
     Yellow                                      0 	        0
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	1
                Green  :	1
                Yellow :	0
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	3
                Green  :	3
                Yellow :	0
                Red    :	0
Fragments:
 Number of matches:     	35
                                          Precursors 	 Products
 Number of PepFrag1 matches:                     2 	       18
     Green                                       2 	       18
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of VarMod matches:                       1 	       17
     Green                                       1 	       17
     Yellow                                      0 	        0
     Red                                         0 	        0
Total processing time: 9.0179277 seconds
