
*******************************************************************************
--------------------------------- IADBs ------------------------------------
--------------------- Copyright © 2008-2015 Waters Corporation ---------------------
Version 2.175 Compiled: 11/19/2015 6:33 PM
Run at: 1/28/2023 10:14 PM
Command Line:

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs5242805640002146195.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs5242805640002146195.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\plgs5242805640002146195.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs5242805640002146195.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\22DEZ22_PLASMA_FRANGO_104.raw"
 Acquired Name: "22DEZ22_PLASMA_FRANGO_104"
 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\22DEZ22_PLASMA_FRANGO_104.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\22dez22_plasma_frango_104_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 22292.95
Precursor MHPlus Window PPM    = 4.485723 (set automatically by resolution)
Product MHPlus Window PPM      = 11.21431 (set automatically by resolution)
Max MHPlus Window PPM          = 22.42862
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 403 LE ions, 6603 HE ions (6603 binned), 400 bins in 0.1557427 seconds
Read 115903 proteins in 4.7655405 seconds
Matched 46 out of 3829946 peptides in digest to 46 matches in 9 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 46 out of 3829946 peptides in digest to 46 matches in 9 of 115903 proteins
After Pass1:  0 distraction, 8 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, 8 regular proteins
After Filter Proteins:  0 distraction, 8 regular proteins

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

Number of hit groups:   	6
Proteins:
 Number of good matches:	8
                Green  :	8
                Yellow :	0
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	85
                Green  :	64
                Yellow :	21
                Red    :	0
Fragments:
 Number of matches:     	838
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    54 	      597
     Green                                      40 	      538
     Yellow                                     14 	       59
     Red                                         0 	        0
 Number of MissedCleavage matches:              11 	       81
     Green                                       8 	       67
     Yellow                                      3 	       14
     Red                                         0 	        0
 Number of VarMod matches:                      18 	      151
     Green                                      14 	      131
     Yellow                                      4 	       20
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              2 	        9
     Green                                       2 	        9
     Yellow                                      0 	        0
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	6
                Green  :	6
                Yellow :	0
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	72
                Green  :	60
                Yellow :	12
                Red    :	0
Fragments:
 Number of matches:     	767
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    45 	      543
     Green                                      37 	      510
     Yellow                                      8 	       33
     Red                                         0 	        0
 Number of MissedCleavage matches:               9 	       74
     Green                                       7 	       65
     Yellow                                      2 	        9
     Red                                         0 	        0
 Number of VarMod matches:                      16 	      141
     Green                                      14 	      131
     Yellow                                      2 	       10
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              2 	        9
     Green                                       2 	        9
     Yellow                                      0 	        0
     Red                                         0 	        0
Total processing time: 9.6288417 seconds
