
*******************************************************************************
--------------------------------- IADBs ------------------------------------
--------------------- Copyright © 2008-2015 Waters Corporation ---------------------
Version 2.175 Compiled: 11/19/2015 6:33 PM
Run at: 1/28/2023 10:07 PM
Command Line:

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs5471345572163088123.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs5471345572163088123.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\plgs5471345572163088123.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs5471345572163088123.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_56.raw"
 Acquired Name: "22DEZ15_PLASMA_FRANGO_56"
 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_56.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_56_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 19352.9
Precursor MHPlus Window PPM    = 5.167184 (set automatically by resolution)
Product MHPlus Window PPM      = 12.91796 (set automatically by resolution)
Max MHPlus Window PPM          = 25.83592
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 361 LE ions, 5945 HE ions (5945 binned), 358 bins in 0.1854754 seconds
Read 115903 proteins in 5.5260259 seconds
Matched 86 out of 3829946 peptides in digest to 86 matches in 58 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 87 out of 3829946 peptides in digest to 87 matches in 58 of 115903 proteins
After Pass1:  4 distraction, 92 regular proteins
Curate calibration disabled : Only found 10 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 -0.5397 Max 1.1201 Mean 0.1046 StdDev 0.8900
fragSimilarity: Min 0.4473 Max 0.7340 Mean 0.5613 StdDev 0.1521
weightedSeqCoverage: Min 0.1667 Max 0.2778 Mean 0.2125 StdDev 0.0580
byTheoretical: Min -3.3671 Max -0.4754 Mean -1.9264 StdDev 1.4459
prodRtErr: Min 0.0000 Max 0.0089 Mean 0.0030 StdDev 0.0051
prodMassErr: Min 0.0000 Max 0.0006 Mean 0.0003 StdDev 0.0003

After Pass2 Depletion:  3 distraction, 88 regular proteins
After Filter Proteins:  3 distraction, 88 regular proteins

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

Number of hit groups:   	15
Proteins:
 Number of good matches:	88
                Green  :	76
                Yellow :	5
                Red    :	7
 Number of distractions:	3
Peptides:
 Number of matches:     	225
                Green  :	164
                Yellow :	19
                Red    :	42
Fragments:
 Number of matches:     	2,604
                                          Precursors 	 Products
 Number of PepFrag1 matches:                   208 	    2,502
     Green                                     159 	    2,272
     Yellow                                     14 	       80
     Red                                        35 	      150
 Number of PepFrag2 matches:                     4 	       18
     Green                                       0 	        0
     Yellow                                      0 	        0
     Red                                         4 	       18
 Number of MissedCleavage matches:               5 	       49
     Green                                       2 	       31
     Yellow                                      0 	        0
     Red                                         3 	       18
 Number of VarMod matches:                       4 	       26
     Green                                       0 	        0
     Yellow                                      4 	       26
     Red                                         0 	        0
 Number of InSource matches:                     3 	        8
     Green                                       2 	        5
     Yellow                                      1 	        3
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              1 	        1
     Green                                       1 	        1
     Yellow                                      0 	        0
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	13
                Green  :	9
                Yellow :	3
                Red    :	1
 Number of distractions:	3
Peptides:
 Number of matches:     	54
                Green  :	25
                Yellow :	17
                Red    :	12
Fragments:
 Number of matches:     	433
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    41 	      353
     Green                                      20 	      245
     Yellow                                     12 	       70
     Red                                         9 	       38
 Number of PepFrag2 matches:                     2 	        8
     Green                                       0 	        0
     Yellow                                      0 	        0
     Red                                         2 	        8
 Number of MissedCleavage matches:               3 	       37
     Green                                       2 	       31
     Yellow                                      0 	        0
     Red                                         1 	        6
 Number of VarMod matches:                       4 	       26
     Green                                       0 	        0
     Yellow                                      4 	       26
     Red                                         0 	        0
 Number of InSource matches:                     3 	        8
     Green                                       2 	        5
     Yellow                                      1 	        3
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              1 	        1
     Green                                       1 	        1
     Yellow                                      0 	        0
     Red                                         0 	        0
Total processing time: 10.6815167 seconds
