

PXD004732 scan 59739 difference between deepprot and specoms

./src/deepprot -p ../test/v20200324/PXD004732_params.csv -m ../test/data/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59739.mgf ../test/data/fasta_59739.fasta  -o test.ods

PXD004732 scan 59739 spectrum int in deepprot :
11007 12008 12910 13008 14711 17511 17908 18314 18516 18608 19508 19712 20112 21114 21117 21316 22515 22717 23917 24311 24411 24416 24512 25318 25322 26019 27610 28820 29817 29917 34018 34117 34124 35518 36923 39325 46830 48324 49828 54026 64635 65738 70237 72434 72538 74191 74239 74244 81139 83245 88243 88343 90350 90450 96450 99553 101659 111565 124569 125968

PXD004732 scan 59739 spectrum int in specoms :
11007 12008 12910 13008 14711 17511 17908 18314 18516 18608 19508 19712 20112 21114 21117 21316 22515 22717 23917 24311 24411 24416 24512 25318 25322 26019 27610 28820 29817 29917 34018 34117 34124 35518 36923 39325 46830 48324 49828 54026 64635 65738 70237 72434 72538 74191 74239 74244 81139 83245 88243 88343 90350 90450 96450 99553 101659 111565 124569 125968

specoms v20200324:
SIPGIDYIDCIRR
(SLPGLDYLDCLRR)
INFOS: SIPGIDYIDCIRR
mars 25, 2020 4:35:34 PM biodata.Spectrum createFromPeptide
INFOS: [8804, *17512*, *20112*, *29818*, 33122, *35520*, 44430, *46828*, 58331, 60433, 71936, 74637, *83245*, 85946, 97448, *99551*, 111054, 113451, 122362, 124760, 128064, 137769, 140370, 149078, 155980, 157781]


specoms ancienne version:
IPSAVAMMIAQIK



deepprot :
SIPGIPYVPVGAIR
PISAVADAIFR
SIPAEWPSDPTTDIHR
IEPSATSNQQQPK
ISPGIGISGFSGGIK
IPSAVAMMIAQIK

SIPGIDYIDCIRR est un missed cleavage, cherché dans spectree, ce que ne fait pas deepprot

c'est bon dans :
https://forgemia.inra.fr/anr-deepprot/deepprot/-/commit/869c36261af70117eef5460e2f5dc8ba8b1a8e58


cmake .. -DCMAKE_BUILD_TYPE=Release
make

./src/deepprot -p ../test/v20200324/PXD004732_params.csv -m /media/langella/pappso/deepprot/donnees/PXD004732/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.mzXML /media/langella/pappso/deepprot/donnees/PXD004732/Araport11_genes.201606.pep.fasta /media/langella/pappso/deepprot/donnees/PXD004732/crapPeptidesRef_Pool65.fasta -o /media/langella/pappso/deepprot/donnees/PXD004732/v20200318/PXD004732_SENSIBLE_T7S9_MIN-500_deepprot.ods



PXD004732 scan 59723 difference between deepprot and specoms

specoms :
01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.raw.59723	IPSGEIVSGSSDASIK	7	8	13	45,0694		 	{ 23763 23764 }	Target
23763 ; >AT3G18860.1 | transducin family protein / WD-40 repeat family protein | Chr3:6501774-6508352 FORWARD LENGTH=760 | 201606
23764 ; >AT3G18860.2 | transducin family protein / WD-40 repeat family protein | Chr3:6501774-6508352 FORWARD LENGTH=760 | 201606


deepprot:
controllerType=0 controllerNumber=1 scan=59723	59722	2	795,935241699219	1589,85593046468	29	NoDeltaPosition	IPSGEIVSGSSDASIK	target	target	IPSGEIVSGSSDASIK	1545,78861676891	773,901584851335	7	7	delta_position	44,0673136957689	5 6 7 8 9 10 11 12 13	47526 47528	AT3G18860.1 AT3G18860.2


msconvert /media/langella/pappso/deepprot/donnees/PXD004732/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.mzXML --mgf --filter "scanNumber 59723"
cp ./01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.mgf ../test/data/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59723.mgf

cd test/java/tests/cmd/PXD004732_59723/

java -server -Xmx4g -jar /home/langella/developpement/git/deepprot/cbuild/bin/SpecOMS.jar -c

test specoms sur jeu réduit :
spectrumID;peptide;sharedMassesBeforeSpecFit;sharedMassesAfterSpecFit;massDeltaLocation;observedMassDelta;affix;cutSide;;proteinsOrigin
01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.59723.59723.2;IPSGEIVSGSSDASIK;7;7;-1;44.0673;; ;{ 0 1 };Target


INFOS: IPSGEIVSGSSDASIK
mars 26, 2020 3:34:53 PM biodata.Spectrum createFromPeptide
INFOS: [11409, 14711, 21114, 26020, 29818, 34723, 35520, 41827, 48424, 53329, 59732, 62032, 69639, 70736, 76438, 78343, 84045, 85141, 92748, 95048, 101451, 106356, 112954, 119261, 120057, 124963, 128761, 133666, 140069, 143371, 152879, 154680]

INFOS: 01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.59723.59723.2
mars 26, 2020 3:44:01 PM biodata.Spectrum createFromIntArray
INFOS: [79641, 24311, 34223, 21114, 34220, 12008, 74039, 24411, 19508, 76841, 64933, 75243, 22911, 75136, 17511, 12910, 35519, 63132, 18314, 47031, 89557, 14711, 50226, 62134, 77842, 48425, 79595, 32218, 22410, 33018, 26115, 22717, 29514, 37328, 18912, 24211, 47725, 110762, 22713, 47426, 26019, 110863, 28915, 33718, 17908, 23510, 73442, 24416, 34819, 35924, 32720, 20413, 36416, 35120, 119260, 32319, 42720, 29817, 23316, 79694]

cmake .. -DCMAKE_BUILD_TYPE=Debug
make -j 8

./src/deepprot -p ../test/v20200324/PXD004732_params.csv -m ../test/data/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59723.mgf ../test/data/fasta_59723.fasta  -o test.ods

/home/langella/developpement/git/deepprot/src/core/spectrumintstore.cpp@133, SpectrumIntStore::newSpectrumIntFromPeptide(): peptide= "IPSGEIVSGSSDASIK"   "IPSGEIVSGSSDASIK\n11409 14711 21114 26020 29818 34723 35520 41827 48424 53329 59732 62032 69639 70736 76438 78342 84045 85141 92748 95048 101451 106356 112954 119261 120057 124963 128761 133666 140069 143371 \n"

pectrumReader::setQualifiedMassSpectrum(): "index=0"   "12008 12910 14711 17511 17908 18314 18912 19508 20413 21114 22410 22713 22717 22911 23316 23510 24211 24311 24411 24416 26019 26115 28915 29514 29817 32218 32319 32720 33018 33718 34220 34223 34819 35120 35519 35924 36416 37328 42720 47031 47426 47725 48425 50226 62134 63132 64933 73442 74039 75136 75243 76841 77842 79595 79641 79694 89557 110762 110863 119260"

Mw = 1546.795

precursor mz = 795.935241699219
charge = 2

795.935241699219 *2 - (1.007276466879) = 1590.863

1590.863 - 1546.795 = 44.068 delta


file:///D:\olivier/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.raw.59678	PINKAETGGIGAGDSK	7	7	-1	83,0131		 	{ 89300 89301 89302 }	Decoy
controllerType=0 controllerNumber=1 scan=59678	59677	2	799,400634765625	1596,78671659749	1	NoDeltaPosition	IINVTIATIDTSK	target	target	IINVTIATIDTSK	1387,79224559703	694,903399265394	7	7	no_delta_position	208,994471000463		2670 2672	AT1G07460.1 AT1G07460.2

msconvert /media/langella/pappso/deepprot/donnees/PXD004732/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.mzXML --mgf --filter "scanNumber 59678"
cp ./01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.mgf ../test/data/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59678.mgf

cd test/java/tests/cmd/PXD004732_59678/


java -server -Xmx4g -jar /home/langella/developpement/git/deepprot/cbuild/bin/SpecOMS.jar -c

INFOS: 01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2.59678.59678.2
mars 31, 2020 3:46:18 PM biodata.Spectrum createFromIntArray
INFOS: [24311, 79941, 24411, 19508, 12910, 14711, 71441, 78139, 73541, 34418, 84543, 23414, 21513, 51822, 17511, 34818, 12008, 38717, 81143, 22713, 21114, 42720, 43519, 53624, 110962, 26115, 79894, 45122, 45319, 55727, 110862, 11007, 13008, 119363, 18314, 45222, 53426, 19608, 34918, 24816, 72546, 23913, 24110, 79986, 31123, 135571, 84644, 22512, 26019, 55423, 54134, 21713, 74336, 65442, 18912, 22717, 16506, 35014, 17908, 49422]


INFOS: PINKAETGGIGAGDSK
mars 31, 2020 3:46:17 PM biodata.Spectrum createFromPeptide
INFOS: [9806, 14711, 21114, 23414, 32519, 34917, 40619, 45328, 47723, 52432, 53425, 64734, 65336, 70436, 75441, 76138, 81143, 86243, 86845, 98154, 99147, 103856, 106251, 110960, 116662, 119060, 128164, 130464, 136868, 141773, 149677, 151478]

INFOS: IINVTIATIDTSK
mars 31, 2020 3:46:17 PM biodata.Spectrum createFromPeptide
INFOS: [11409, 14711, 22718, 23414, 33519, 34122, 44029, 45022, 54133, 56330, 65442, 66435, 72546, 73539, 82650, 84847, 93959, 94952, 104859, 105461, 115566, 116263, 124269, 127571, 137079, 138880]


cmake .. -DCMAKE_BUILD_TYPE=Debug
make
./src/deepprot -p ../test/v20200324/PXD004732_params.csv -m ../test/data/01650b_BG3-TUM_first_pool_65_01_01-DDA-1h-R2-59678.mgf ../test/data/fasta_59678.fasta  -o test.ods

60
/home/langella/developpement/git/deepprot/src/core/msspectrumreader.cpp@145, MsSpectrumReader::setQualifiedMassSpectrum(): "index=0"   "11007 12008 12910 13008 14711 16506 17511 17908 18314 18912 19508 19608 21114 21513 21713 22512 22713 22717 23414 23913 24110 24311 24411 24816 26019 26115 31123 34418 34818 34918 35014 38717 42720 43519 45122 45222 45319 49422 51822 53426 53624 54134 55423 55727 65442 71441 72546 73541 74336 78139 79894 79941 79986 81143 84543 84644 110862 110962 119363 135571"

/home/langella/developpement/git/deepprot/src/core/fastasourcelist.cpp@147, FastaSourceList::protoPeptideProduct(): "AT5G21160.1"   "PINKAETGGIGAGDSK"   5
/home/langella/developpement/git/deepprot/src/core/spectrumintstore.cpp@133, SpectrumIntStore::newSpectrumIntFromPeptide(): peptide= "PINKAETGGIGAGDSK"   "PINKAETGGIGAGDSK\n9806 +14711 +21114 +23414 32519 +34917 40619 45328 47723 52432 +53425 64734 65336 70436 75441 76138 +81143 86243 86845 98154 99147 103856 106251 *110959* 116662 119060 128164 130464 136868 141773 \n"
=> 6

/home/langella/developpement/git/deepprot/src/core/spectrumintstore.cpp@133, SpectrumIntStore::newSpectrumIntFromPeptide(): peptide= "IINVTIATIDTSK"   "IINVTIATIDTSK\n11409 +14711 +22718 +23414 33519 34122 44029 45022 +54133 56330 +65442 66435 +72546 +73539 82650 84847 93959 94952 104859 105461 115566 116263 124269 127572 \n"
=> 7
