#FILE	./MSups_5ul_b.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	0.165
# CUTOFF	PROBABILITY	0.10	FPR	0.116
# CUTOFF	PROBABILITY	0.20	FPR	0.116
# CUTOFF	PROBABILITY	0.30	FPR	0.076
# CUTOFF	PROBABILITY	0.40	FPR	0.057
# CUTOFF	PROBABILITY	0.50	FPR	0.041
# CUTOFF	PROBABILITY	0.60	FPR	0.041
# CUTOFF	PROBABILITY	0.70	FPR	0.031
# CUTOFF	PROBABILITY	0.80	FPR	0.024
# CUTOFF	PROBABILITY	0.90	FPR	0.005
# CUTOFF	PROBABILITY	0.95	FPR	0.002
# CUTOFF	PROBABILITY	0.96	FPR	0.002
# 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	0.50	0.40	0.057	0.041
# PROBABILITY CUT (0.05 FDR)	0.4437
# UPPER PROB, LOWER PROB, UPPER FPR, LOWER FPR	0.50	0.40	0.057	0.041
# PROBABILITY CUT (0.05 FDR)	0.4437
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	1604
# TOTAL NUMBER OF (CONTRIBUTING) PEPTIDE COUNTS	185
# 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	0.8530	6	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	14	4	1	DMASNYKELGFQG HGATVLTALGGILK HGATVLTALGGILKK VEADIPGHGQEVLIRLFKGHPETLEK	MYG_HUMAN_UPS	P02144ups
PROTEIN	4	EGF_HUMAN_UPS	0.9423	12	1	1	DLKWWELR	EGF_HUMAN_UPS	P01133ups
PROTEIN	5	HBA_HUMAN_UPS	1.0000	21	4	1	FLASVSTVLTSK MFLSFPTTK VADALTNAVAHVDDMPNALSALSDLHAHK VGAHAGEYGAEALER	HBA_HUMAN_UPS	P69905ups
PROTEIN	6	TRFE_HUMAN_UPS	0.9686	1	1	1	PVVAEFYGSKEDPQTFYYAVAVVKK	TRFE_HUMAN_UPS	P02787ups
PROTEIN	7	NQO1_HUMAN_UPS	0.9978	5	2	1	IQILEGWK IQILEGWKK	NQO1_HUMAN_UPS	P15559ups
PROTEIN	8	PPIA_HUMAN_UPS	1.0000	38	10	1	EGMNIVEAMER FEDENFILK IIPGFMCQGGDFTR IIPGFMCQGGDFTRHNGTGGK ITIADCGQLE KITIADCGQLE TEWLDGKHVVFGK VKEGMNIVEAMER VSFELFADK VSFELFADKVPK	PPIA_HUMAN_UPS	P62937ups
PROTEIN	9	NEDD8_HUMAN_UPS	0.7727	1	1	1	EIEIDIEPTDKVER	NEDD8_HUMAN_UPS	Q15843ups
PROTEIN	10	shuff1_CATA_HUMAN_UPS	0.6770	1	2	1	AHTDVIFSSVNYSAVLDLGNDAGRE VINPGKIIFTDAEEATR	shuff1_CATA_HUMAN_UPS	P04040ups
PROTEIN	11	shuff1_NQO1_HUMAN_UPS	0.9955	1	1	1	AESDRSFQLLSLPDPMEFNFPSKEK	shuff1_NQO1_HUMAN_UPS	P15559ups
PROTEIN	12	KCRM_HUMAN_UPS	1.0000	18	10	1	ELFDPIISDR GQSIDDMIPAQK LNYKPEEEYPDLSK LSVEALNSLTGEFK LSVEALNSLTGEFKGK PVSPLLLASGMARDWPDAR RGTGGVDTAAVGSVFDVSNADR SFLVWVNEEDHLR TDLNHENLKGGDDLDPNYVLSSR VLTLELYK	KCRM_HUMAN_UPS	P06732ups
PROTEIN	13	CAH2_HUMAN_UPS	1.0000	167	12	1	AVQQPDGLAVLGIFLK EPISVSSEQVLK GGPLDGTYR GKSADFTNFDPR LIQFHFHWGSLDGQGSEHTVDK LIQFHFHWGSLDGQGSEHTVDKK QSPVDIDTHTAK QSPVDIDTHTAKYDPSLKPLSVSYDQATSLR SADFTNFDPR YAAELHLVHWNTK YAAELHLVHWNTKYGDFGK YDPSLKPLSVSYDQATSLR	CAH2_HUMAN_UPS	P00918ups
PROTEIN	14	UBC9_HUMAN_UPS	0.9998	7	3	1	GTPWEGGLFK KDHPFGFVAVPTK MLFKDDYPSSPPK	UBC9_HUMAN_UPS	P63279ups
PROTEIN	15	LEP_HUMAN_UPS	1.0000	114	3	1	DLLHVLAFSK NVIQISNDLENLR QKVTGLDFIPGLHPILTLSK	LEP_HUMAN_UPS	P41159ups
PROTEIN	16	SUMO1_HUMAN_UPS	1.0000	28	11	1	AEISMLEGAVLDIR DFETLKVDFLSK ERAEISMLEGAVLDIR FLFEGQR IAYSKDFETLK IAYSKDFETLKVDFLSK IEAIPQIDKYLK LLLEYLEEK LTQSMAIIR MSPILGYWK RIEAIPQIDKYLK	SUMO1_HUMAN_UPS	P63165ups
PROTEIN	17	BID_HUMAN_UPS	0.9955	1	1	1	NRDLATALEQLLQAYPRDMEK	BID_HUMAN_UPS	P55957ups
PROTEIN	18	HBB_HUMAN_UPS	1.0000	56	9	1	EFTPPVQAAYQK GTFATLSELHCDK KVLGAFSDGLAHLDNLK LLGNVLVCVLAHHFGK LLVVYPWTQR SAVTALWGK VNVDEVGGEALGR VVAGVANALAHK VVAGVANALAHKYH	HBB_HUMAN_UPS	P68871ups
PROTEIN	19	LALBA_HUMAN_UPS	0.8395	2	1	1	ALCTEKLEQWLCEK	LALBA_HUMAN_UPS	P00709ups
PROTEIN	20	CYC_HUMAN_UPS	0.8930	1	2	1	IFIMKCSQCHTVEK NKGIIWGEDTLMEYLENPKK	CYC_HUMAN_UPS	P99999ups
PROTEIN	21	shuff1_KCRM_HUMAN_UPS	0.4644	1	1	1	RLQHTSHNKICK	shuff1_KCRM_HUMAN_UPS	P06732ups
PROTEIN	22	CAH1_HUMAN_UPS	1.0000	257	15	1	ADGLAVIGVLMK EIINVGHSFHVNFEDNDNR EIINVGHSFHVNFEDNDNRSVLK ESISVSSEQLAQFR GGPFSDSYR HDTSLKPISVSYNPATAK LFQFHFHWGSTNEHGSEHTVDGVK LYPIANGNNQSPVDIK LYPIANGNNQSPVDIKTSETK SLLSNVEGDNAVPMQHNNR SLLSNVEGDNAVPMQHNNRPTQPLK SLLSNVEGDNAVPMQHNNRPTQPLKGR TSETKHDTSLKPISVSYNPATAK YSAELHVAHWNSAK YSSLAEAASK	CAH1_HUMAN_UPS	P00915ups
PROTEIN	23	SYHC_HUMAN_UPS	1.0000	11	8	1	ASAELIEEEVAK HGAEVIDTPVFELK IFSIVEQR ILDGMFAICGVSDSK RHGAEVIDTPVFELK VFDVIIR VPCVGLSIGVER YDLTVPFAR	SYHC_HUMAN_UPS	P12081ups
PROTEIN	24	CYB5_HUMAN_UPS	0.8466	6	2	1	TFIIGELHPDDRPK YYTLEEIQK	CYB5_HUMAN_UPS	P00167ups
PROTEIN	25	shuff1_ANXA5_HUMAN_UPS	0.9955	1	1	1	LTQYDSTLVVQGVQLTAK	shuff1_ANXA5_HUMAN_UPS	P08758ups
PROTEIN	26	NQO2_HUMAN_UPS	0.9955	1	1	1	VLAPQISFAPEIASEEER	NQO2_HUMAN_UPS	P16083ups
PROTEIN	27	shuff1_CATD_HUMAN_UPS	0.9955	1	1	1	CPRDPLRDVVATFALGEPAPISSEQMR	shuff1_CATD_HUMAN_UPS	P07339ups
PROTEIN	28	PRDX1_HUMAN_UPS	1.0000	42	12	1	ATAVMPDGQFK ATAVMPDGQFKDISLSDYKGK GLFIIDDK KLNCQVIGASVDSHFCHLAWVNTPK KQGGLGPMNIPLVSDPK KQGGLGPMNIPLVSDPKR LNCQVIGASVDSHFCHLAWVNTPKK LVQAFQFTDK QGGLGPMNIPLVSDPK QGGLGPMNIPLVSDPKR QITVNDLPVGR TIAQDYGVLK	PRDX1_HUMAN_UPS	Q06830ups
PROTEIN	29	CATA_HUMAN_UPS	1.0000	66	20	1	AAQKADVLTTGAGNPVGDKLNVITVGPR ADVLTTGAGNPVGDKLNVITVGPR AFYVNVLNEEQR AFYVNVLNEEQRK DPILFPSFIHSQK DYPLIPVGK FNTANDDNVTQVR GAGAFGYFEVTHDITK GAGAFGYFEVTHDITKYSK GPLLVQDVVFTDEMAHFDR GPLLVQDVVFTDEMAHFDRER LCENIAGHLKDAQIFIQK LCENIAGHLKDAQIFIQKK LFAYPDTHR LGPNYLHIPVNCPYR LSQEDPDYGIR LVNANGEAVYCK NAIHTFVQSGSHLAAR NFTEVHPDYGSHIQALLDK NFTEVHPDYGSHIQALLDKYNAEKPK	CATA_HUMAN_UPS	P04040ups
PROTEIN	30	UBIQ_HUMAN_UPS	1.0000	12	4	1	QLEDGRTLSDYNIQK TITLEVEPSDTIENVKAK TLSDYNIQK TLSDYNIQKESTLHLVLR	UBIQ_HUMAN_UPS	P62988ups
PROTEIN	31	ALBU_HUMAN_UPS	1.0000	672	34	1	AACLLPK AEFAEVSKLVTDLTK AVMDDFAAFVEK CCTESLVNR CCTESLVNRRPCFSALEVDETYVPK FKDLGEENFK FPKAEFAEVSK HPDYSVVLLLR HPYFYAPELLFFAK HPYFYAPELLFFAKR KLVAASQAALGL KQTALVELVK LCTVATLR LDELRDEGK LKECCEKPLLEK LVAASQAALGL LVNEVTEFAK LVRPEVDVMCTAFHDNEETFLK LVRPEVDVMCTAFHDNEETFLKK NECFLQHKDDNPNLPR PCFSALEVDETYVPK PLVEEPQNLIK QNCELFEQLGEYK QTALVELVK RHPDYSVVLLLR RHPYFYAPELLFFAK RHPYFYAPELLFFAKR RPCFSALEVDETYVPK SLHTLFGDKLCTVATLR VFDEFKPLVEEPQNLIK VPQVSTPTLVEVSR YKAAFTECCQAADKAACLLPK YLYEIAR YTKKVPQVSTPTLVEVSR	ALBU_HUMAN_UPS	P02768ups