
*******************************************************************************
--------------------------------- IADBs ------------------------------------
--------------------- Copyright © 2008-2015 Waters Corporation ---------------------
Version 2.175 Compiled: 11/19/2015 6:33 PM
Run at: 1/28/2023 10:21 PM
Command Line:

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs3850638836842139054.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs3850638836842139054.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\plgs3850638836842139054.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs3850638836842139054.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_71.raw"
 Acquired Name: "22DEZ15_PLASMA_FRANGO_71"
 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_71.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_71_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 20101.86
Precursor MHPlus Window PPM    = 4.974665 (set automatically by resolution)
Product MHPlus Window PPM      = 12.43666 (set automatically by resolution)
Max MHPlus Window PPM          = 24.87332
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, 3330 HE ions (3330 binned), 183 bins in 0.1119369 seconds
Read 115903 proteins in 5.0025214 seconds
Matched 28 out of 3829946 peptides in digest to 28 matches in 12 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 28 out of 3829946 peptides in digest to 28 matches in 11 of 115903 proteins
After Pass1:  1 distraction, 74 regular proteins
Curate calibration disabled : Only found 3 distraction peptides
Yellow-Green Threshold = 6 Red-Yellow Threshold = 5

Statistics:
pepBinomial: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000
precModelRT: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000
precMassErr: Min -0.7397 Max -0.7397 Mean -0.7397 StdDev 0.0000
fragSimilarity: Min 0.3432 Max 0.3432 Mean 0.3432 StdDev 0.0000
weightedSeqCoverage: Min 0.8571 Max 0.8571 Mean 0.8571 StdDev 0.0000
byTheoretical: Min -1.7190 Max -1.7190 Mean -1.7190 StdDev 0.0000
prodRtErr: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000
prodMassErr: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000

After Pass2 Depletion:  1 distraction, 72 regular proteins
After Filter Proteins:  1 distraction, 72 regular proteins

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

Number of hit groups:   	5
Proteins:
 Number of good matches:	72
                Green  :	72
                Yellow :	0
                Red    :	0
 Number of distractions:	1
Peptides:
 Number of matches:     	148
                Green  :	139
                Yellow :	9
                Red    :	0
Fragments:
 Number of matches:     	1,633
                                          Precursors 	 Products
 Number of PepFrag1 matches:                   143 	    1,604
     Green                                     135 	    1,554
     Yellow                                      8 	       50
     Red                                         0 	        0
 Number of MissedCleavage matches:               1 	        9
     Green                                       1 	        9
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of VarMod matches:                       2 	       19
     Green                                       1 	       14
     Yellow                                      1 	        5
     Red                                         0 	        0
 Number of InSource matches:                     2 	        1
     Green                                       2 	        1
     Yellow                                      0 	        0
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	4
                Green  :	4
                Yellow :	0
                Red    :	0
 Number of distractions:	1
Peptides:
 Number of matches:     	28
                Green  :	19
                Yellow :	9
                Red    :	0
Fragments:
 Number of matches:     	233
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    23 	      204
     Green                                      15 	      154
     Yellow                                      8 	       50
     Red                                         0 	        0
 Number of MissedCleavage matches:               1 	        9
     Green                                       1 	        9
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of VarMod matches:                       2 	       19
     Green                                       1 	       14
     Yellow                                      1 	        5
     Red                                         0 	        0
 Number of InSource matches:                     2 	        1
     Green                                       2 	        1
     Yellow                                      0 	        0
     Red                                         0 	        0
Total processing time: 9.891693 seconds
