#FILE	./MSups_5ul_c.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	0.140
# CUTOFF	PROBABILITY	0.10	FPR	0.073
# CUTOFF	PROBABILITY	0.20	FPR	0.073
# CUTOFF	PROBABILITY	0.30	FPR	0.073
# CUTOFF	PROBABILITY	0.40	FPR	0.025
# CUTOFF	PROBABILITY	0.50	FPR	0.011
# CUTOFF	PROBABILITY	0.60	FPR	0.011
# CUTOFF	PROBABILITY	0.70	FPR	0.011
# CUTOFF	PROBABILITY	0.80	FPR	0.011
# CUTOFF	PROBABILITY	0.90	FPR	0.003
# CUTOFF	PROBABILITY	0.95	FPR	0.001
# CUTOFF	PROBABILITY	0.96	FPR	0.001
# CUTOFF	PROBABILITY	0.97	FPR	0.001
# 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	0.40	0.30	0.073	0.025
# PROBABILITY CUT (0.05 FDR)	0.3479
# UPPER PROB, LOWER PROB, UPPER FPR, LOWER FPR	0.40	0.30	0.073	0.025
# PROBABILITY CUT (0.05 FDR)	0.3479
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	1879
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	189
# 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	0.8785	6	1	1	FSGTWYAMAK	RETBP_HUMAN_UPS	P02753ups
PROTEIN	2	CO5_HUMAN_UPS	1.0000	61	2	1	AFTECCVVASQLR CIKAFTECCVVASQLR	CO5_HUMAN_UPS	P01031ups
PROTEIN	3	THIO_HUMAN_UPS	0.9963	1	1	1	HHHHHHVKQIESKTAFQEALDAAGDK	THIO_HUMAN_UPS	P10599ups
PROTEIN	4	MYG_HUMAN_UPS	1.0000	20	5	1	DMASNYKELGFQG GLSDGEWQLVLNVWGK HGATVLTALGGILK HGATVLTALGGILKK YLEFISECIIQVLQSK	MYG_HUMAN_UPS	P02144ups
PROTEIN	5	EGF_HUMAN_UPS	0.3926	6	1	1	DLKWWELR	EGF_HUMAN_UPS	P01133ups
PROTEIN	6	HBA_HUMAN_UPS	1.0000	23	4	1	FLASVSTVLTSK MFLSFPTTK VADALTNAVAHVDDMPNALSALSDLHAHK VGAHAGEYGAEALER	HBA_HUMAN_UPS	P69905ups
PROTEIN	7	TRFE_HUMAN_UPS	1.0000	2	2	1	PVEEYANCHLARAPNHAVVTRK PVVAEFYGSKEDPQTFYYAVAVVK	TRFE_HUMAN_UPS	P02787ups
PROTEIN	8	UBE2C_HUMAN_UPS	1.0000	9	2	1	FLTPCYHPNVDTQGNICLDILK KYLQETYSKQVTSQEP	UBE2C_HUMAN_UPS	O00762ups
PROTEIN	9	NQO1_HUMAN_UPS	0.9996	4	3	1	ALIVLAHSERTSFNYAMKEAAAAALK IQILEGWK IQILEGWKK	NQO1_HUMAN_UPS	P15559ups
PROTEIN	10	PPIA_HUMAN_UPS	1.0000	36	8	1	FEDENFILK IIPGFMCQGGDFTR ITIADCGQLE KITIADCGQLE TEWLDGKHVVFGK VKEGMNIVEAMER VSFELFADK VSFELFADKVPK	PPIA_HUMAN_UPS	P62937ups
PROTEIN	11	NEDD8_HUMAN_UPS	0.9942	3	2	1	EIEIDIEPTDKVER TLTGKEIEIDIEPTDKVER	NEDD8_HUMAN_UPS	Q15843ups
PROTEIN	12	shuff1_CATA_HUMAN_UPS	0.9963	1	1	1	AHTDVIFSSVNYSAVLDLGNDAGRE	shuff1_CATA_HUMAN_UPS	P04040ups
PROTEIN	13	CRP_HUMAN_UPS	0.9919	1	1	1	GYSIFSYATKRQDNEILIFWSK	CRP_HUMAN_UPS	P02741ups
PROTEIN	14	shuff1_NQO2_HUMAN_UPS	1.0000	2	2	1	CDSTLEPTVVSNAYGRSPAGAHSPR HWADAAQEDFTKKEDIENFQITAK	shuff1_NQO2_HUMAN_UPS	P16083ups
PROTEIN	15	UBC9_HUMAN_UPS	0.8532	2	1	1	MLFKDDYPSSPPK	UBC9_HUMAN_UPS	P63279ups
PROTEIN	16	KCRM_HUMAN_UPS	1.0000	20	11	1	ELFDPIISDR FKLNYKPEEEYPDLSK HKTDLNHENLKGGDDLDPNYVLSSR LNYKPEEEYPDLSK LSVEALNSLTGEFK LSVEALNSLTGEFKGK PVSPLLLASGMARDWPDAR RFCVGLQKIEEIFK RGTGGVDTAAVGSVFDVSNADR SFLVWVNEEDHLR TDLNHENLKGGDDLDPNYVLSSR	KCRM_HUMAN_UPS	P06732ups
PROTEIN	17	CAH2_HUMAN_UPS	1.0000	230	11	1	AVQQPDGLAVLGIFLK EPISVSSEQVLK GGPLDGTYR ILNNGHAFNVEFDDSQDKAVLK LIQFHFHWGSLDGQGSEHTVDK LIQFHFHWGSLDGQGSEHTVDKK QSPVDIDTHTAKYDPSLKPLSVSYDQATSLR SADFTNFDPR YAAELHLVHWNTK YAAELHLVHWNTKYGDFGK YDPSLKPLSVSYDQATSLR	CAH2_HUMAN_UPS	P00918ups
PROTEIN	18	LEP_HUMAN_UPS	1.0000	138	4	1	DLLHVLAFSK LQGSLQDMLWQLDLSPGC NVIQISNDLENLR QKVTGLDFIPGLHPILTLSK	LEP_HUMAN_UPS	P41159ups
PROTEIN	19	SUMO1_HUMAN_UPS	1.0000	24	9	1	AEISMLEGAVLDIR DFETLKVDFLSK FLFEGQR IAYSKDFETLK IAYSKDFETLKVDFLSK LLLEYLEEK LLLEYLEEKYEEHLYER MSPILGYWK RIEAIPQIDKYLK	SUMO1_HUMAN_UPS	P63165ups
PROTEIN	20	BID_HUMAN_UPS	0.9963	6	1	1	NRDLATALEQLLQAYPRDMEK	BID_HUMAN_UPS	P55957ups
PROTEIN	21	HBB_HUMAN_UPS	1.0000	68	8	1	EFTPPVQAAYQK FFESFGDLSTPDAVMGNPK GTFATLSELHCDK KVLGAFSDGLAHLDNLK LLVVYPWTQR SAVTALWGK VNVDEVGGEALGR VVAGVANALAHK	HBB_HUMAN_UPS	P68871ups
PROTEIN	22	CYC_HUMAN_UPS	0.4740	2	2	1	IFIMKCSQCHTVEK YIPGTKMIFVGIKK	CYC_HUMAN_UPS	P99999ups
PROTEIN	23	CAH1_HUMAN_UPS	1.0000	300	13	1	ADGLAVIGVLMK EIINVGHSFHVNFEDNDNR EIINVGHSFHVNFEDNDNRSVLK ESISVSSEQLAQFR GGPFSDSYR HDTSLKPISVSYNPATAK LFQFHFHWGSTNEHGSEHTVDGVK LYPIANGNNQSPVDIK LYPIANGNNQSPVDIKTSETK SLLSNVEGDNAVPMQHNNRPTQPLK SLLSNVEGDNAVPMQHNNRPTQPLKGR TSETKHDTSLKPISVSYNPATAK YSSLAEAASK	CAH1_HUMAN_UPS	P00915ups
PROTEIN	24	SYHC_HUMAN_UPS	1.0000	9	4	1	EEVDVRREDLVEEIK HGAEVIDTPVFELK ILDGMFAICGVSDSK QALEGLGDLKLLFEYLTLFGIDDK	SYHC_HUMAN_UPS	P12081ups
PROTEIN	25	CYB5_HUMAN_UPS	0.9977	5	2	1	TFIIGELHPDDRPK YYTLEEIQK	CYB5_HUMAN_UPS	P00167ups
PROTEIN	26	shuff1_B2MG_HUMAN_UPS	0.9963	1	1	1	VLPNTAYSVLGHYDCSKK	shuff1_B2MG_HUMAN_UPS	P61769ups
PROTEIN	27	shuff1_GELS_HUMAN_UPS	0.9963	1	1	1	NAFARLVGTVGYGASTRSATGLESK	shuff1_GELS_HUMAN_UPS	P06396ups
PROTEIN	28	shuff1_ANXA5_HUMAN_UPS	0.9963	1	1	1	LTQYDSTLVVQGVQLTAK	shuff1_ANXA5_HUMAN_UPS	P08758ups
PROTEIN	29	shuff1_TRFE_HUMAN_UPS	0.9963	1	1	1	EEGDHLAGVGKKPNCACCTFK	shuff1_TRFE_HUMAN_UPS	P02787ups
PROTEIN	30	NQO2_HUMAN_UPS	0.9963	1	1	1	VLAPQISFAPEIASEEER	NQO2_HUMAN_UPS	P16083ups
PROTEIN	31	shuff1_CATD_HUMAN_UPS	0.9999	2	1	1	CPRDPLRDVVATFALGEPAPISSEQMR	shuff1_CATD_HUMAN_UPS	P07339ups
PROTEIN	32	PRDX1_HUMAN_UPS	1.0000	39	13	1	ADEGISFRGLFIIDDK ATAVMPDGQFK ATAVMPDGQFKDISLSDYKGK GLFIIDDK KLNCQVIGASVDSHFCHLAWVNTPK KQGGLGPMNIPLVSDPK KQGGLGPMNIPLVSDPKR LNCQVIGASVDSHFCHLAWVNTPKK LVQAFQFTDK QGGLGPMNIPLVSDPK QITVNDLPVGR TIAQDYGVLK TIAQDYGVLKADEGISFR	PRDX1_HUMAN_UPS	Q06830ups
PROTEIN	33	shuff1_UBE2C_HUMAN_UPS	1.0000	2	2	1	AEEASYMIVLPSTYGHQLASFMVKQDR PTLGQTPSLDGAEAAGTKYGPNHK	shuff1_UBE2C_HUMAN_UPS	O00762ups
PROTEIN	34	CATA_HUMAN_UPS	1.0000	79	19	1	AAQKADVLTTGAGNPVGDKLNVITVGPR ADVLTTGAGNPVGDKLNVITVGPR AFYVNVLNEEQR AFYVNVLNEEQRK DPILFPSFIHSQK DPILFPSFIHSQKR DYPLIPVGK FNTANDDNVTQVR FSTVAGESGSADTVRDPR GAGAFGYFEVTHDITK GPLLVQDVVFTDEMAHFDR GPLLVQDVVFTDEMAHFDRER LCENIAGHLKDAQIFIQK LCENIAGHLKDAQIFIQKK LGPNYLHIPVNCPYR LSQEDPDYGIR NAIHTFVQSGSHLAAR NFTEVHPDYGSHIQALLDK NFTEVHPDYGSHIQALLDKYNAEKPK	CATA_HUMAN_UPS	P04040ups
PROTEIN	35	UBIQ_HUMAN_UPS	1.0000	11	4	1	QLEDGRTLSDYNIQK QLEDGRTLSDYNIQKESTLHLVLR TITLEVEPSDTIENVKAK TLSDYNIQKESTLHLVLR	UBIQ_HUMAN_UPS	P62988ups
PROTEIN	36	shuff1_TNFA_HUMAN_UPS	0.9373	2	1	1	DQLAPFEVTVVEGPLSAAEFSYSVK	shuff1_TNFA_HUMAN_UPS	P01375ups
PROTEIN	37	ALBU_HUMAN_UPS	1.0000	758	38	1	AACLLPK AEFAEVSK AEFAEVSKLVTDLTK ALVLIAFAQYLQQCPFEDHVK ATKEQLKAVMDDFAAFVEK AVMDDFAAFVEK CCTESLVNR CCTESLVNRRPCFSALEVDETYVPK FKDLGEENFK HPDYSVVLLLR HPYFYAPELLFFAK HPYFYAPELLFFAKR KLVAASQAALGL KQTALVELVK LCTVATLR LKECCEKPLLEK LVAASQAALGL LVNEVTEFAK LVRPEVDVMCTAFHDNEETFLK LVRPEVDVMCTAFHDNEETFLKK MPCAEDYLSVVLNQLCVLHEK PCFSALEVDETYVPK PLVEEPQNLIK QNCELFEQLGEYK QNCELFEQLGEYKFQNALLVR QTALVELVK RHPDYSVVLLLR RHPYFYAPELLFFAK RMPCAEDYLSVVLNQLCVLHEK RPCFSALEVDETYVPK SLHTLFGDKLCTVATLR TYETTLEKCCAAADPHECYAK VFDEFKPLVEEPQNLIK VPQVSTPTLVEVSR YKAAFTECCQAADKAACLLPK YLYEIAR YLYEIARR YTKKVPQVSTPTLVEVSR	ALBU_HUMAN_UPS	P02768ups