#FILE	./MSups_30ul.prot.xml
#PROTEIN	Number	Name	Probability	Total peptide counts	Unique peptides	No. indistinguishable proteins	Peptides	Degenerate Proteins	Annotation
# DATABASE	/project/marcotte/marcotte/ms/database/ms_ups2_sp_CON_shuff.fasta
# CUTOFF	PROBABILITY	0.00	FPR	0.430
# CUTOFF	PROBABILITY	0.10	FPR	0.152
# CUTOFF	PROBABILITY	0.20	FPR	0.152
# CUTOFF	PROBABILITY	0.30	FPR	0.079
# CUTOFF	PROBABILITY	0.40	FPR	0.065
# CUTOFF	PROBABILITY	0.50	FPR	0.040
# CUTOFF	PROBABILITY	0.60	FPR	0.028
# CUTOFF	PROBABILITY	0.70	FPR	0.011
# CUTOFF	PROBABILITY	0.80	FPR	0.006
# CUTOFF	PROBABILITY	0.90	FPR	0.006
# CUTOFF	PROBABILITY	0.95	FPR	0.006
# CUTOFF	PROBABILITY	0.96	FPR	0.006
# CUTOFF	PROBABILITY	0.97	FPR	0.004
# CUTOFF	PROBABILITY	0.98	FPR	0.003
# CUTOFF	PROBABILITY	0.99	FPR	0.000
# CUTOFF	PROBABILITY	1.00	FPR	0.000
# UPPER PROB, LOWER PROB, UPPER FPR, LOWER FPR	0.50	0.40	0.065	0.040
# PROBABILITY CUT (0.05 FDR)	0.46
# UPPER PROB, LOWER PROB, UPPER FPR, LOWER FPR	0.50	0.40	0.065	0.040
# PROBABILITY CUT (0.05 FDR)	0.46
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	2588
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	337
# PROTEIN	Number	Name	Probability	Contributing_spectral_counts	All_unique_peptides	No._indistinguishable_proteins	Peptides	Degenerate Proteins	Annotation
#	PEPTIDE	Protein_Name	PeptideSequence_Charge	Degenerate?	Spectral counts	Contributing?	Adjusted NPS prob	Weight_(degeneracy)
# DATA
PROTEIN	1	RETBP_HUMAN_UPS	0.9673	6	4	1	DPNGLPPEAQK LLNLDGTCADSYSFVFSR MKYWGVASFLQK YWGVASFLQK	RETBP_HUMAN_UPS	P02753ups
PROTEIN	2	PDGFB_HUMAN_UPS	0.9998	2	2	1	ATVTLEDHLACKCETVAAARPVT TNANFLVWPPCVEVQR	PDGFB_HUMAN_UPS	P01127ups
PROTEIN	3	HBA_HUMAN_UPS	1.0000	43	7	1	FLASVSTVLTSK MFLSFPTTK TYFPHFDLSHGSAQVK VADALTNAVAHVDDMPNALSALSDLHAHK VADALTNAVAHVDDMPNALSALSDLHAHKLR VDPVNFK VGAHAGEYGAEALER	HBA_HUMAN_UPS	P69905ups
PROTEIN	4	TRFE_HUMAN_UPS	1.0000	6	6	1	APNHAVVTR DSAHGFLKVPPRMDAK KPVEEYANCHLARAPNHAVVTR PVKWCALSHHERLK PVVAEFYGSKEDPQTFYYAVAVVK YLGEEYVK	TRFE_HUMAN_UPS	P02787ups
PROTEIN	5	UBE2C_HUMAN_UPS	0.9654	1	3	1	FLTPCYHPNVDTQGNICLDILK GAEPSGGAARGPVGK KYLQETYSKQVTSQEP	UBE2C_HUMAN_UPS	O00762ups
PROTEIN	6	NQO1_HUMAN_UPS	0.9999	5	4	1	ALIVLAHSERTSFNYAMK EAAAAALKKK IQILEGWK VFIGEFAYTYAAMYDK	NQO1_HUMAN_UPS	P15559ups
PROTEIN	7	shuff1_NQO1_HUMAN_UPS	0.9998	5	3	1	AESDRSFQLLSLPDPMEFNFPSKEK FLPFLADHK VIMWMQGYMAIGAIFFHADSVEDGHR	shuff1_NQO1_HUMAN_UPS	P15559ups
PROTEIN	8	CRP_HUMAN_UPS	0.6655	6	2	1	ESDTSYVSLK GYSIFSYATKRQDNEILIFWSK	CRP_HUMAN_UPS	P02741ups
PROTEIN	9	UBC9_HUMAN_UPS	0.7928	6	4	1	DHPFGFVAVPTK GTPWEGGLFK KGTPWEGGLFK MLFKDDYPSSPPK	UBC9_HUMAN_UPS	P63279ups
PROTEIN	10	KCRM_HUMAN_UPS	1.0000	33	14	1	AGHPFMWNQHLGYVLTCPSNLGTGLR FCVGLQK GGDDLDPNYVLSSR GGDDLDPNYVLSSRVRTGR GTGGVDTAAVGSVFDVSNADR HKTDLNHENLKGGDDLDPNYVLSSR LAHLSKHPK LGSSEVEQVQLVVDGVK LNYKPEEEYPDLSK LSVEALNSLTGEFK LSVEALNSLTGEFKGK SFLVWVNEEDHLR VLTLELYK VLTLELYKK	KCRM_HUMAN_UPS	P06732ups
PROTEIN	11	HBB_HUMAN_UPS	1.0000	69	10	1	EFTPPVQAAYQK FFESFGDLSTPDAVMGNPK GTFATLSELHCDK KVLGAFSDGLAHLDNLK LLVVYPWTQR SAVTALWGK VLGAFSDGLAHLDNLK VNVDEVGGEALGR VVAGVANALAHK VVAGVANALAHKYH	HBB_HUMAN_UPS	P68871ups
PROTEIN	12	TRFL_HUMAN_UPS	0.9909	10	7	1	DCHLARVPSHAVVAR FFSASCVPGADK GPPVSCIKR KPVTEAR QAQEKFGK THYYAVAVVK TTYEKYLGPQYVAGITNLKK	TRFL_HUMAN_UPS	P02788ups
PROTEIN	13	shuff1_KCRM_HUMAN_UPS	0.9898	1	1	1	FFEPKRLQHTSHNK	shuff1_KCRM_HUMAN_UPS	P06732ups
PROTEIN	14	CYB5_HUMAN_UPS	1.0000	4	2	1	EMSKTFIIGELHPDDRPK TFIIGELHPDDRPK	CYB5_HUMAN_UPS	P00167ups
PROTEIN	15	shuff1_GELS_HUMAN_UPS	0.9898	1	2	1	FFATHNAYKDTGVETLK IEKDRALELLHGEEPSAEEDLASR	shuff1_GELS_HUMAN_UPS	P06396ups
PROTEIN	16	shuff1_TRFE_HUMAN_UPS	0.9898	1	2	1	FVSGLPNVADCRDLK GYGGFKTRK	shuff1_TRFE_HUMAN_UPS	P02787ups
PROTEIN	17	shuff1_TRFL_HUMAN_UPS	0.9896	1	4	1	EGIGSVKLVLEKPR GNNQKGSRLSWGK TYVSPNTWALECVDVPSGQPARFSIR VGRRELSFGGR	shuff1_TRFL_HUMAN_UPS	P02788ups
PROTEIN	18	PRDX1_HUMAN_UPS	1.0000	46	16	1	ATAVMPDGQFK ATAVMPDGQFKDISLSDYK ATAVMPDGQFKDISLSDYKGK GLFIIDDK GLFIIDDKGILR KLNCQVIGASVDSHFCHLAWVNTPK KLNCQVIGASVDSHFCHLAWVNTPKK KQGGLGPMNIPLVSDPK KQGGLGPMNIPLVSDPKR LNCQVIGASVDSHFCHLAWVNTPKK LVQAFQFTDK QGGLGPMNIPLVSDPK QGGLGPMNIPLVSDPKR QITVNDLPVGR TIAQDYGVLK TIAQDYGVLKADEGISFR	PRDX1_HUMAN_UPS	Q06830ups
PROTEIN	19	UBIQ_HUMAN_UPS	1.0000	35	4	1	TITLEVEPSDTIENVK TITLEVEPSDTIENVKAK TLSDYNIQK TLSDYNIQKESTLHLVLR	UBIQ_HUMAN_UPS	P62988ups
PROTEIN	20	ALBU_HUMAN_UPS	1.0000	1128	55	1	AACLLPK AAFTECCQAADK AAFTECCQAADKAACLLPK ADDKETCFAEEGKK AEFAEVSK AEFAEVSKLVTDLTK ALVLIAFAQYLQQCPFEDHVK AVMDDFAAFVEK CCTESLVNR CCTESLVNRRPCFSALEVDETYVPK DDNPNLPR DVFLGMFLYEYAR EFNAETFTFHADICTLSEK EFNAETFTFHADICTLSEKERQIK EQLKAVMDDFAAFVEK ETYGEMADCCAK FKDLGEENFK FQNALLVR HPDYSVVLLLR HPYFYAPELLFFAK HPYFYAPELLFFAKR KLVAASQAALGL KQTALVELVK KVPQVSTPTLVEVSR LCTVATLR LDELRDEGK LKECCEKPLLEK LSQRFPK LVAASQAALGL LVNEVTEFAK LVRPEVDVMCTAFHDNEETFLK LVRPEVDVMCTAFHDNEETFLKK LVTDLTK MPCAEDYLSVVLNQLCVLHEK PCFSALEVDETYVPK PLVEEPQNLIK QEPERNECFLQHK QNCELFEQLGEYK QNCELFEQLGEYKFQNALLVR QTALVELVK RHPDYSVVLLLR RHPYFYAPELLFFAK RMPCAEDYLSVVLNQLCVLHEK RPCFSALEVDETYVPK SLHTLFGDK SLHTLFGDKLCTVATLR TCVADESAENCDK TYETTLEK VFDEFKPLVEEPQNLIK VPQVSTPTLVEVSR YICENQDSISSK YKAAFTECCQAADK YKAAFTECCQAADKAACLLPK YLYEIAR YTKKVPQVSTPTLVEVSR	ALBU_HUMAN_UPS	P02768ups
PROTEIN	21	shuff1_SYHC_HUMAN_UPS	0.5225	1	3	1	ALEITTTK DEVIWLVK EDEVTKCTYGPEVIR	shuff1_SYHC_HUMAN_UPS	P12081ups
PROTEIN	22	CO5_HUMAN_UPS	1.0000	73	4	1	AFTECCVVASQLR CCYDGACVNNDETCEQR CIKAFTECCVVASQLR IEEIAAK	CO5_HUMAN_UPS	P01031ups
PROTEIN	23	MYG_HUMAN_UPS	1.0000	27	8	1	DMASNYKELGFQG FDKFKHLK GLSDGEWQLVLNVWGK HGATVLTALGGILK HGATVLTALGGILKK VEADIPGHGQEVLIR VEADIPGHGQEVLIRLFKGHPETLEK YLEFISECIIQVLQSK	MYG_HUMAN_UPS	P02144ups
PROTEIN	24	EGF_HUMAN_UPS	0.9822	30	2	1	DLKWWELR YACNCVVGYIGER	EGF_HUMAN_UPS	P01133ups
PROTEIN	25	PPIA_HUMAN_UPS	1.0000	50	8	1	EGMNIVEAMER FEDENFILK IIPGFMCQGGDFTR SIYGEKFEDENFILK TEWLDGKHVVFGK VKEGMNIVEAMER VSFELFADK VSFELFADKVPK	PPIA_HUMAN_UPS	P62937ups
PROTEIN	26	shuff1_CRP_HUMAN_UPS	0.9898	1	2	1	NKSVPKGNMYWAK SSHGFVWFLPDARAGK	shuff1_CRP_HUMAN_UPS	P02741ups
PROTEIN	27	shuff1_NQO2_HUMAN_UPS	0.9729	1	2	1	AFVNPQPK CDSTLEPTVVSNAYGRSPAGAHSPR	shuff1_NQO2_HUMAN_UPS	P16083ups
PROTEIN	28	CAH2_HUMAN_UPS	1.0000	221	12	1	AVQQPDGLAVLGIFLK EPISVSSEQVLK GGPLDGTYR KYAAELHLVHWNTKYGDFGK LIQFHFHWGSLDGQGSEHTVDK QSPVDIDTHTAK QSPVDIDTHTAKYDPSLKPLSVSYDQATSLR SADFTNFDPR VVDVLDSIK YAAELHLVHWNTK YAAELHLVHWNTKYGDFGK YDPSLKPLSVSYDQATSLR	CAH2_HUMAN_UPS	P00918ups
PROTEIN	29	SUMO1_HUMAN_UPS	1.0000	37	17	1	AEISMLEGAVLDIR DFETLKVDFLSK ERAEISMLEGAVLDIR FLFEGQR IAYSKDFETLKVDFLSK IEAIPQIDKYLK IEAIPQIDKYLKSSK LLLEYLEEK LLLEYLEEKYEEHLYER LTQSMAIIR MSPILGYWK QGVPMNSLR RIEAIPQIDKYLK VDFLSKLPEMLK VDFLSKLPEMLKMFEDR VKMTTHLK YGVSRIAYSKDFETLK	SUMO1_HUMAN_UPS	P63165ups
PROTEIN	30	LEP_HUMAN_UPS	1.0000	267	7	1	DLLHVLAFSK INDISHTQSVSSK LQGSLQDMLWQLDLSPGC MDQTLAVYQQILTSMPSR NVIQISNDLENLR QKVTGLDFIPGLHPILTLSK VTGLDFIPGLHPILTLSK	LEP_HUMAN_UPS	P41159ups
PROTEIN	31	BID_HUMAN_UPS	0.9992	3	2	1	DECITNLLVFGFLQSCSDNSFRR NRDLATALEQLLQAYPRDMEK	BID_HUMAN_UPS	P55957ups
PROTEIN	32	shuff1_HBA_HUMAN_UPS	0.9898	1	1	1	DSYVCDKFDLGLHVENALFVTAALGSK	shuff1_HBA_HUMAN_UPS	P69905ups
PROTEIN	33	LALBA_HUMAN_UPS	0.6689	2	4	1	ALCTEKLEQWLCEK ALCTEKLEQWLCEKL GIDYWLAHK LEQWLCEKL	LALBA_HUMAN_UPS	P00709ups
PROTEIN	34	CAH1_HUMAN_UPS	1.0000	312	18	1	ADGLAVIGVLMK ADGLAVIGVLMKVGEANPK EIINVGHSFHVNFEDNDNR EIINVGHSFHVNFEDNDNRSVLK ESISVSSEQLAQFR GGPFSDSYR HDTSLKPISVSYNPATAK LFQFHFHWGSTNEHGSEHTVDGVK LQKVLDALQAIK LYPIANGNNQSPVDIK LYPIANGNNQSPVDIKTSETK LYPIANGNNQSPVDIKTSETKHDTSLK SLLSNVEGDNAVPMQHNNRPTQPLK SLLSNVEGDNAVPMQHNNRPTQPLKGR TSETKHDTSLKPISVSYNPATAK VLDALQAIK YSAELHVAHWNSAK YSSLAEAASK	CAH1_HUMAN_UPS	P00915ups
PROTEIN	35	SYHC_HUMAN_UPS	1.0000	21	9	1	EDLVEEIK EKVFDVIIR HGAEVIDTPVFELK ILDGMFAICGVSDSK ISFDLSLAR LVSELWDAGIKAELLYK RHGAEVIDTPVFELK VPCVGLSIGVER YDLTVPFAR	SYHC_HUMAN_UPS	P12081ups
PROTEIN	36	NQO2_HUMAN_UPS	1.0000	6	3	1	LALLSVTTGGTAEMYTK NVAVDELSR VLAPQISFAPEIASEEER	NQO2_HUMAN_UPS	P16083ups
PROTEIN	37	shuff1_HBB_HUMAN_UPS	0.9898	1	1	1	TAPTVPLPALVELTDK	shuff1_HBB_HUMAN_UPS	P68871ups
PROTEIN	38	CATA_HUMAN_UPS	1.0000	99	26	1	AAQKADVLTTGAGNPVGDKLNVITVGPR ADVLTTGAGNPVGDKLNVITVGPR AFYVNVLNEEQR AFYVNVLNEEQRK DAQIFIQK DLFNAIATGK DPILFPSFIHSQK DPILFPSFIHSQKR DYPLIPVGK FNTANDDNVTQVR FSTVAGESGSADTVRDPR GAGAFGYFEVTHDITK GAGAFGYFEVTHDITKYSK GPLLVQDVVFTDEMAHFDRER LCENIAGHLKDAQIFIQK LCENIAGHLKDAQIFIQKK LFAYPDTHR LGPNYLHIPVNCPYR LSQEDPDYGIR LVNANGEAVYCK NAIHTFVQSGSHLAAR NFTEVHPDYGSHIQALLDK NFTEVHPDYGSHIQALLDKYNAEKPK NLSVEDAAR VFEHIGKK VWPHKDYPLIPVGK	CATA_HUMAN_UPS	P04040ups
PROTEIN	39	GELS_HUMAN_UPS	1.0000	7	8	1	AALKTASDFITK DPDQTDGLGLSYLSSHIANVER EPAHLMSLFGGKPMIIYKGGTSR GASQAGAPQGR LFQVKGRR RTPITVVK TPSAAYLWVGTGASEAEK VHVSEEGTEPEAMLQVLGPK	GELS_HUMAN_UPS	P06396ups