
*******************************************************************************
--------------------------------- IADBs ------------------------------------
--------------------- Copyright © 2008-2015 Waters Corporation ---------------------
Version 2.175 Compiled: 11/19/2015 6:33 PM
Run at: 1/27/2023 1:46 PM
Command Line:

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs4156953175005223964.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs4156953175005223964.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\plgs4156953175005223964.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs4156953175005223964.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_3.raw"
 Acquired Name: "22DEZ15_PLASMA_FRANGO_3"
 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: 1/27/2023
    command line: "C:\PLGS3.0.3\lib\apex3d\Apex3D64.exe" -pRawDirName "G:\JOSE_SPOTS_DEZ22\22DEZ15_PLASMA_FRANGO_3.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: 1/27/2023
    command line: C:\PLGS3.0.3\lib\apex3d\Peptide3D.exe -inputFilename C:\Users\Administrator\AppData\Local\Temp\22dez15_plasma_frango_3_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 21140.46
Precursor MHPlus Window PPM    = 4.730265 (set automatically by resolution)
Product MHPlus Window PPM      = 11.82566 (set automatically by resolution)
Max MHPlus Window PPM          = 23.65133
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 484 LE ions, 10196 HE ions (10196 binned), 483 bins in 0.2073249 seconds
Read 115903 proteins in 5.3548669 seconds
Matched 39 out of 3829946 peptides in digest to 39 matches in 29 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 39 out of 3829946 peptides in digest to 39 matches in 29 of 115903 proteins
After Pass1:  4 distraction, 9 regular proteins
Curate calibration disabled : Only found 12 distraction peptides
Yellow-Green Threshold = 6 Red-Yellow Threshold = 5

Statistics:
pepBinomial: Min 0.0000 Max 0.0016 Mean 0.0010 StdDev 0.0009
precModelRT: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000
precMassErr: Min -1.0040 Max -0.1970 Mean -0.6537 StdDev 0.4139
fragSimilarity: Min 0.7462 Max 0.9919 Mean 0.8987 StdDev 0.1332
weightedSeqCoverage: Min 0.0385 Max 0.1500 Mean 0.0850 StdDev 0.0580
byTheoretical: Min -0.2084 Max 0.5828 Mean 0.1097 StdDev 0.4177
prodRtErr: Min 0.0000 Max 0.2781 Mean 0.1689 StdDev 0.1484
prodMassErr: Min 0.0002 Max 0.4984 Mean 0.2221 StdDev 0.2535

After Pass2 Depletion:  1 distraction, 7 regular proteins
After Filter Proteins:  0 distraction, 6 regular proteins

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

Number of hit groups:   	5
Proteins:
 Number of good matches:	6
                Green  :	2
                Yellow :	1
                Red    :	3
 Number of distractions:	0
Peptides:
 Number of matches:     	9
                Green  :	3
                Yellow :	1
                Red    :	5
Fragments:
 Number of matches:     	97
                                          Precursors 	 Products
 Number of PepFrag1 matches:                     7 	       87
     Green                                       3 	       50
     Yellow                                      1 	        7
     Red                                         3 	       30
 Number of PepFrag2 matches:                     2 	       10
     Green                                       0 	        0
     Yellow                                      0 	        0
     Red                                         2 	       10
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	5
                Green  :	2
                Yellow :	1
                Red    :	2
 Number of distractions:	0
Peptides:
 Number of matches:     	7
                Green  :	3
                Yellow :	1
                Red    :	3
Fragments:
 Number of matches:     	81
                                          Precursors 	 Products
 Number of PepFrag1 matches:                     6 	       76
     Green                                       3 	       50
     Yellow                                      1 	        7
     Red                                         2 	       19
 Number of PepFrag2 matches:                     1 	        5
     Green                                       0 	        0
     Yellow                                      0 	        0
     Red                                         1 	        5
Total processing time: 10.386708 seconds
