#FILE	./MSups_5ul_dynex.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	0.113
# CUTOFF	PROBABILITY	0.10	FPR	0.033
# CUTOFF	PROBABILITY	0.20	FPR	0.033
# CUTOFF	PROBABILITY	0.30	FPR	0.033
# CUTOFF	PROBABILITY	0.40	FPR	0.033
# CUTOFF	PROBABILITY	0.50	FPR	0.033
# CUTOFF	PROBABILITY	0.60	FPR	0.033
# CUTOFF	PROBABILITY	0.70	FPR	0.026
# CUTOFF	PROBABILITY	0.80	FPR	0.026
# CUTOFF	PROBABILITY	0.90	FPR	0.011
# CUTOFF	PROBABILITY	0.95	FPR	0.003
# CUTOFF	PROBABILITY	0.96	FPR	0.003
# CUTOFF	PROBABILITY	0.97	FPR	0.003
# CUTOFF	PROBABILITY	0.98	FPR	0.001
# CUTOFF	PROBABILITY	0.99	FPR	0.001
# CUTOFF	PROBABILITY	1.00	FPR	0.000
# UPPER PROB, LOWER PROB, UPPER FPR, LOWER FPR	0.10	0.00	0.113	0.033
# PROBABILITY CUT (0.05 FDR)	0.0787
# UPPER PROB, LOWER PROB, UPPER FPR, LOWER FPR	0.10	0.00	0.113	0.033
# PROBABILITY CUT (0.05 FDR)	0.0787
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	1360
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	194
# 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	0.9083	4	1	1	FSGTWYAMAK	RETBP_HUMAN_UPS	P02753ups
PROTEIN	2	CO5_HUMAN_UPS	1.0000	35	2	1	AFTECCVVASQLR CIKAFTECCVVASQLR	CO5_HUMAN_UPS	P01031ups
PROTEIN	3	MYG_HUMAN_UPS	1.0000	21	4	1	DMASNYKELGFQG HGATVLTALGGILK HGATVLTALGGILKK KGHHEAEIKPLAQSHATK	MYG_HUMAN_UPS	P02144ups
PROTEIN	4	EGF_HUMAN_UPS	0.9715	8	1	1	DLKWWELR	EGF_HUMAN_UPS	P01133ups
PROTEIN	5	PDGFB_HUMAN_UPS	0.9970	1	1	1	ATVTLEDHLACKCETVAAARPVT	PDGFB_HUMAN_UPS	P01127ups
PROTEIN	6	HBA_HUMAN_UPS	1.0000	13	4	1	FLASVSTVLTSK MFLSFPTTK VADALTNAVAHVDDMPNALSALSDLHAHK VGAHAGEYGAEALER	HBA_HUMAN_UPS	P69905ups
PROTEIN	7	TRFE_HUMAN_UPS	0.9919	1	2	1	DLLFRDDTVCLAK PVVAEFYGSKEDPQTFYYAVAVVKK	TRFE_HUMAN_UPS	P02787ups
PROTEIN	8	UBE2C_HUMAN_UPS	0.9973	5	1	1	KYLQETYSKQVTSQEP	UBE2C_HUMAN_UPS	O00762ups
PROTEIN	9	NQO1_HUMAN_UPS	0.9982	2	3	1	ALIVLAHSERTSFNYAMK IQILEGWK IQILEGWKK	NQO1_HUMAN_UPS	P15559ups
PROTEIN	10	PPIA_HUMAN_UPS	1.0000	28	9	1	FEDENFILK IIPGFMCQGGDFTR ITIADCGQLE KITIADCGQLE TEWLDGKHVVFGK VKEGMNIVEAMER VSFELFADK VSFELFADKVPK VSFELFADKVPKTAENFR	PPIA_HUMAN_UPS	P62937ups
PROTEIN	11	NEDD8_HUMAN_UPS	0.8982	3	1	1	EIEIDIEPTDKVER	NEDD8_HUMAN_UPS	Q15843ups
PROTEIN	12	LYSC_HUMAN_UPS	0.9973	1	1	1	LGMDGYRGISLANWMCLAK	LYSC_HUMAN_UPS	P61626ups
PROTEIN	13	shuff1_NQO2_HUMAN_UPS	0.9973	1	1	1	CDSTLEPTVVSNAYGRSPAGAHSPR	shuff1_NQO2_HUMAN_UPS	P16083ups
PROTEIN	14	CRP_HUMAN_UPS	0.9973	1	1	1	GYSIFSYATKRQDNEILIFWSK	CRP_HUMAN_UPS	P02741ups
PROTEIN	15	UBC9_HUMAN_UPS	0.6677	2	2	1	GTPWEGGLFK MLFKDDYPSSPPK	UBC9_HUMAN_UPS	P63279ups
PROTEIN	16	shuff1_CATG_HUMAN_UPS	0.9336	1	1	1	GRPFFIGWNWLHFSLMANG	shuff1_CATG_HUMAN_UPS	P08311ups
PROTEIN	17	KCRM_HUMAN_UPS	1.0000	16	8	1	ELFDPIISDR LNYKPEEEYPDLSK LSVEALNSLTGEFK LSVEALNSLTGEFKGK PVSPLLLASGMARDWPDAR RGTGGVDTAAVGSVFDVSNADR SFLVWVNEEDHLR TDLNHENLKGGDDLDPNYVLSSR	KCRM_HUMAN_UPS	P06732ups
PROTEIN	18	CAH2_HUMAN_UPS	1.0000	155	9	1	AVQQPDGLAVLGIFLK EPISVSSEQVLK LIQFHFHWGSLDGQGSEHTVDK QSPVDIDTHTAK QSPVDIDTHTAKYDPSLKPLSVSYDQATSLR SADFTNFDPR YAAELHLVHWNTK YAAELHLVHWNTKYGDFGK YDPSLKPLSVSYDQATSLR	CAH2_HUMAN_UPS	P00918ups
PROTEIN	19	LEP_HUMAN_UPS	1.0000	95	4	1	DLLHVLAFSK INDISHTQSVSSK NVIQISNDLENLR QKVTGLDFIPGLHPILTLSK	LEP_HUMAN_UPS	P41159ups
PROTEIN	20	SUMO1_HUMAN_UPS	1.0000	23	12	1	AEISMLEGAVLDIR DFETLKVDFLSK ERAEISMLEGAVLDIR FLFEGQR IAYSKDFETLKVDFLSK IEAIPQIDKYLK LLLEYLEEK LLLEYLEEKYEEHLYER LTQSMAIIR MSPILGYWK QGVPMNSLRFLFEGQRIADNHTPK RIEAIPQIDKYLK	SUMO1_HUMAN_UPS	P63165ups
PROTEIN	21	BID_HUMAN_UPS	0.9227	1	1	1	IEADSESQEDIIRNIAR	BID_HUMAN_UPS	P55957ups
PROTEIN	22	LALBA_HUMAN_UPS	0.8932	1	1	1	ALCTEKLEQWLCEK	LALBA_HUMAN_UPS	P00709ups
PROTEIN	23	HBB_HUMAN_UPS	1.0000	32	8	1	EFTPPVQAAYQK GTFATLSELHCDK KVLGAFSDGLAHLDNLK LLGNVLVCVLAHHFGK LLVVYPWTQR SAVTALWGK VNVDEVGGEALGR VVAGVANALAHK	HBB_HUMAN_UPS	P68871ups
PROTEIN	24	UB2E1_HUMAN_UPS	0.9910	1	1	1	ASTSSSSSSSSNQQTEKETNTPKK	UB2E1_HUMAN_UPS	P51965ups
PROTEIN	25	TRFL_HUMAN_UPS	0.9973	2	1	1	TTYEKYLGPQYVAGITNLKK	TRFL_HUMAN_UPS	P02788ups
PROTEIN	26	shuff1_KCRM_HUMAN_UPS	0.8130	3	1	1	RLQHTSHNKICK	shuff1_KCRM_HUMAN_UPS	P06732ups
PROTEIN	27	CAH1_HUMAN_UPS	1.0000	215	15	1	ADGLAVIGVLMK ADGLAVIGVLMKVGEANPK EIINVGHSFHVNFEDNDNR EIINVGHSFHVNFEDNDNRSVLK ESISVSSEQLAQFR GGPFSDSYR HDTSLKPISVSYNPATAK LFQFHFHWGSTNEHGSEHTVDGVK LYPIANGNNQSPVDIK LYPIANGNNQSPVDIKTSETK SLLSNVEGDNAVPMQHNNRPTQPLK SLLSNVEGDNAVPMQHNNRPTQPLKGR TSETKHDTSLKPISVSYNPATAK YSAELHVAHWNSAKYSSLAEAASK YSSLAEAASK	CAH1_HUMAN_UPS	P00915ups
PROTEIN	28	SYHC_HUMAN_UPS	1.0000	12	6	1	HGAEVIDTPVFELK IFSIVEQR ILDGMFAICGVSDSK KVPCVGLSIGVER VFDVIIR YDLTVPFAR	SYHC_HUMAN_UPS	P12081ups
PROTEIN	29	CYB5_HUMAN_UPS	0.8380	4	1	1	YYTLEEIQK	CYB5_HUMAN_UPS	P00167ups
PROTEIN	30	shuff1_GELS_HUMAN_UPS	1.0000	4	2	1	IEKDRALELLHGEEPSAEEDLASR NAFARLVGTVGYGASTRSATGLESK	shuff1_GELS_HUMAN_UPS	P06396ups
PROTEIN	31	CATG_HUMAN_UPS	0.9985	2	3	1	HPQYNQRTIQNDIMLLQLSRR NRNVNPVALPR PHSRPYMAYLQIQSPAGQSR	CATG_HUMAN_UPS	P08311ups
PROTEIN	32	shuff1_TRFL_HUMAN_UPS	0.9777	1	1	1	LVVSDEQPSENTHTPLQPVR	shuff1_TRFL_HUMAN_UPS	P02788ups
PROTEIN	33	shuff1_TRFE_HUMAN_UPS	1.0000	2	2	1	EEGDHLAGVGKKPNCACCTFK PTDAKTSPCLTADVLFVTCREDK	shuff1_TRFE_HUMAN_UPS	P02787ups
PROTEIN	34	NQO2_HUMAN_UPS	1.0000	5	4	1	LQTIWKEEPIPCTAHWHFGQ NVAVDELSRQGCTVTVSDLYAMNFEPR QGCTVTVSDLYAMNFEPRATDK VLAPQISFAPEIASEEER	NQO2_HUMAN_UPS	P16083ups
PROTEIN	35	shuff1_THIO_HUMAN_UPS	0.9973	1	1	1	QQNAAFNEKLKSVEHDVVK	shuff1_THIO_HUMAN_UPS	P10599ups
PROTEIN	36	shuff1_CATD_HUMAN_UPS	0.9321	1	1	1	CPRDPLRDVVATFALGEPAPISSEQMR	shuff1_CATD_HUMAN_UPS	P07339ups
PROTEIN	37	shuff1_CYC_HUMAN_UPS	0.9973	2	1	1	ENPQGTHKNDWGTEIKK	shuff1_CYC_HUMAN_UPS	P99999ups
PROTEIN	38	PRDX1_HUMAN_UPS	1.0000	40	14	1	ATAVMPDGQFKDISLSDYKGK GLFIIDDK GLFIIDDKGILR KLNCQVIGASVDSHFCHLAWVNTPK KLNCQVIGASVDSHFCHLAWVNTPKK KQGGLGPMNIPLVSDPK KQGGLGPMNIPLVSDPKR LNCQVIGASVDSHFCHLAWVNTPKK LVQAFQFTDK QGGLGPMNIPLVSDPK QGGLGPMNIPLVSDPKR QITVNDLPVGR TIAQDYGVLK TIAQDYGVLKADEGISFR	PRDX1_HUMAN_UPS	Q06830ups
PROTEIN	39	shuff1_UBE2C_HUMAN_UPS	0.9973	1	1	1	PTLGQTPSLDGAEAAGTKYGPNHK	shuff1_UBE2C_HUMAN_UPS	O00762ups
PROTEIN	40	CATA_HUMAN_UPS	1.0000	68	19	1	AAQKADVLTTGAGNPVGDKLNVITVGPR ADVLTTGAGNPVGDKLNVITVGPR AFYVNVLNEEQR DPILFPSFIHSQK DPILFPSFIHSQKR DYPLIPVGK FNTANDDNVTQVR GAGAFGYFEVTHDITK GAGAFGYFEVTHDITKYSK GPLLVQDVVFTDEMAHFDR GPLLVQDVVFTDEMAHFDRER LCENIAGHLKDAQIFIQK LCENIAGHLKDAQIFIQKK LFAYPDTHR LGPNYLHIPVNCPYR LVNANGEAVYCK NAIHTFVQSGSHLAAR NFTEVHPDYGSHIQALLDK NFTEVHPDYGSHIQALLDKYNAEKPK	CATA_HUMAN_UPS	P04040ups
PROTEIN	41	UBIQ_HUMAN_UPS	1.0000	10	3	1	TITLEVEPSDTIENVKAK TLSDYNIQK TLSDYNIQKESTLHLVLR	UBIQ_HUMAN_UPS	P62988ups
PROTEIN	42	shuff1_RETBP_HUMAN_UPS	0.8479	1	1	1	SFEQRALQLSTYQKHK	shuff1_RETBP_HUMAN_UPS	P02753ups
PROTEIN	43	GELS_HUMAN_UPS	0.9998	2	2	1	DPDQTDGLGLSYLSSHIANVER EPAHLMSLFGGKPMIIYKGGTSR	GELS_HUMAN_UPS	P06396ups
PROTEIN	44	ALBU_HUMAN_UPS	1.0000	533	32	1	AACLLPK AEFAEVSKLVTDLTK ATKEQLKAVMDDFAAFVEK AVMDDFAAFVEK CCTESLVNR CCTESLVNRRPCFSALEVDETYVPK DLGEENFK HPDYSVVLLLR HPYFYAPELLFFAK HPYFYAPELLFFAKR KLVAASQAALGL LCTVATLR LKECCEKPLLEK LVAASQAALGL LVNEVTEFAK LVNEVTEFAKTCVADESAENCDK LVRPEVDVMCTAFHDNEETFLK LVRPEVDVMCTAFHDNEETFLKK PCFSALEVDETYVPK PLVEEPQNLIK QNCELFEQLGEYK QTALVELVK RHPDYSVVLLLR RHPYFYAPELLFFAK RPCFSALEVDETYVPK SLHTLFGDKLCTVATLR VFDEFKPLVEEPQNLIK VPQVSTPTLVEVSR YKAAFTECCQAADK YKAAFTECCQAADKAACLLPK YLYEIAR YTKKVPQVSTPTLVEVSR	ALBU_HUMAN_UPS	P02768ups