
*******************************************************************************
--------------------------------- IADBs ------------------------------------
--------------------- Copyright © 2008-2015 Waters Corporation ---------------------
Version 2.175 Compiled: 11/19/2015 6:33 PM
Run at: 1/28/2023 10:15 PM
Command Line:

-paraXMLFileName C:\Users\Administrator\AppData\Local\Temp\plgs5347084097296065983.params -pep3DFilename C:\Users\Administrator\AppData\Local\Temp\plgs5347084097296065983.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\plgs5347084097296065983.params"
 Spectrum  Bin File:       "C:\Users\Administrator\AppData\Local\Temp\plgs5347084097296065983.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_105.raw"
 Acquired Name: "22DEZ22_PLASMA_FRANGO_105"
 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_105.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_105_Apex3D.bin -outputDirName C:\Users\Administrator\AppData\Local\Temp -minLEMHPlus 350.0
                   -maxCPUs 12 -clusMzFwhmFraction 0.1428 -amrtMzFwhmFraction 0.219 -amrtChFWHMFraction 0.25


Resolution                     = 22455.08
Precursor MHPlus Window PPM    = 4.453336 (set automatically by resolution)
Product MHPlus Window PPM      = 11.13334 (set automatically by resolution)
Max MHPlus Window PPM          = 22.26668
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 1111 LE ions, 22918 HE ions (22918 binned), 1109 bins in 0.4350273 seconds
Read 115903 proteins in 4.976365 seconds
Matched 334 out of 3829946 peptides in digest to 334 matches in 226 of 115903 proteins
Insufficient pass 0 matches for mass cal
Matched 332 out of 3829946 peptides in digest to 332 matches in 226 of 115903 proteins
After Pass1:  36 distraction, 146 regular proteins

Calibrating AutoCurate Thresholds using 163 distraction peptides
Median Random pepScore 3.094203 Std Random pepScore 0.6285889
Red-Yellow Threshold is 4.67 which is 2.50 stddevs above the mean
Yellow-Green Threshold is 5.61 which is 4.00 stddevs above the mean
Median Random raw pepScore 112.5242 Std Random raw pepScore 191.4787

Statistics:
pepBinomial: Min 0.0000 Max 0.3619 Mean 0.0282 StdDev 0.0737
precModelRT: Min 0.0000 Max 0.0000 Mean 0.0000 StdDev 0.0000
precMassErr: Min -4.0434 Max 3.7371 Mean 0.0615 StdDev 1.6876
fragSimilarity: Min 0.2101 Max 0.9516 Mean 0.7164 StdDev 0.1881
weightedSeqCoverage: Min 0.0000 Max 0.2667 Mean 0.0395 StdDev 0.0583
byTheoretical: Min -2.3205 Max 1.0000 Mean -0.0050 StdDev 0.7829
prodRtErr: Min 0.0000 Max 0.8858 Mean 0.1038 StdDev 0.2203
prodMassErr: Min 0.0000 Max 1.0000 Mean 0.1577 StdDev 0.2644

After Pass2 Depletion:  17 distraction, 90 regular proteins
After Filter Proteins:  0 distraction, 7 regular proteins

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

Number of hit groups:   	3
Proteins:
 Number of good matches:	7
                Green  :	5
                Yellow :	2
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	102
                Green  :	90
                Yellow :	7
                Red    :	5
Fragments:
 Number of matches:     	1,446
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    57 	    1,075
     Green                                      50 	    1,039
     Yellow                                      7 	       36
     Red                                         0 	        0
 Number of PepFrag2 matches:                     1 	        2
     Green                                       0 	        0
     Yellow                                      0 	        0
     Red                                         1 	        2
 Number of MissedCleavage matches:              18 	      200
     Green                                      14 	      184
     Yellow                                      0 	        0
     Red                                         4 	       16
 Number of VarMod matches:                       6 	      115
     Green                                       6 	      115
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of InSource matches:                    17 	       45
     Green                                      17 	       45
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              2 	        6
     Green                                       2 	        6
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of NeutralLoss_NH3 matches:              1 	        3
     Green                                       1 	        3
     Yellow                                      0 	        0
     Red                                         0 	        0
********************************************************************************
Non Homologous:
Proteins:
 Number of good matches:	4
                Green  :	3
                Yellow :	1
                Red    :	0
 Number of distractions:	0
Peptides:
 Number of matches:     	69
                Green  :	60
                Yellow :	6
                Red    :	3
Fragments:
 Number of matches:     	804
                                          Precursors 	 Products
 Number of PepFrag1 matches:                    34 	      578
     Green                                      28 	      551
     Yellow                                      6 	       27
     Red                                         0 	        0
 Number of PepFrag2 matches:                     1 	        2
     Green                                       0 	        0
     Yellow                                      0 	        0
     Red                                         1 	        2
 Number of MissedCleavage matches:              10 	      106
     Green                                       8 	       98
     Yellow                                      0 	        0
     Red                                         2 	        8
 Number of VarMod matches:                       4 	       64
     Green                                       4 	       64
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of InSource matches:                    17 	       45
     Green                                      17 	       45
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of NeutralLoss_H2O matches:              2 	        6
     Green                                       2 	        6
     Yellow                                      0 	        0
     Red                                         0 	        0
 Number of NeutralLoss_NH3 matches:              1 	        3
     Green                                       1 	        3
     Yellow                                      0 	        0
     Red                                         0 	        0
Total processing time: 11.0891144 seconds
