Improved Label-Free LC-MS Analysis by Wavelet-Based Noise Rejection

Table 2

List of the peptides identified using the include lists from unprocessed and processed data. Bold italic proteins indicate abundance variations in agreement with previous outcomes [13].

(a) Over-expressed proteins in hyperevaporative dry eye patients

Name	Entry name	m/z	Charge	Sequence	Score
					Unprocessed	Processed
Hemoglobin subunit bete	HBB_HUMAN	590.89	2	GVANALAHKYH	16	18
		862.91	3	GTFATLSELHCDKLHVDPENFR	40	59
		637.89	2	LLVVYPWTQR	31	30
		737.508	3	TLSELHCDKLHVDPENFR	51	—
		725.44	2	VVAGVANALAHKYH	33	27
		835.59	2	VLGAFSDGLAHLDNLK	—	74
		1030.15	2	FFESFGDLSTPDAVMGNPK	—	17
		888.95	2	LLGNVLVCVLAHHFGK	—	49
		899.64	2	KVLGAFSDGLAHLDNLK	—	53
		575.39	2	VVAGVANALAHK	—	28
		524.805	2	VVYPWTQR	—	14
		810.203	3	FATLSELHCDKLHVDPENFR	—	15
		626.39	2	AGVANALAHKYH	—	17
		786.03	2	LGAFSDGLAHLDNLK	—	22
		Total number of peptides			5	13
		Protein score			86	169
Serum albumin	ALBU_HUMAN	756.49	2	VPQVSTPTLVEVSR	47	—
		613.88	2	FKDLGEENFK	5	17
		717.46	2	KECCEKPLLEK	51	23
		820.49	2	KVPQVSTPTLVEVSR	—	85
		722.35	2	YICENQDSISSK	—	30
		871.95	2	HPYFYAPELLFFAK	—	35
		926.8	3	LVRPEVDVMCTAFHDNEETFLKK	—	29
		Total number of peptides			3	6
		Protein score			71	96
Hemoglobin subunit alpha	HBA_HUMAN	523.96	3	FPHFDLSHGSAQVK	—	2
		663.37	2	HFDLSHGSAQVK	—	30
		942.98	3	DALTNAVAHVDDMPNALSALSDLHAHK	—	46
		785.92	4	KVADALTNAVAHVDDMPNALSALSDLHAHK	—	6
		Total number of peptides			—	4
		Protein score			—	55

(b) Under-expressed proteins in hyperevaporative dry eye patients

Name	Entry name	m/z	Charge	Sequence	Score
					Unprocessed	Processed
Lipocalin-1	LCN1_HUMAN	669.86	2	TDEPGKYTADGGK	34	48
		722.94	2	YCEGELHGKPVR	16	—
		707.44	3	DHYIFYCEGELHGKPVR	97	36
		643.64	4	SHVKDHYIFYCEGELHGKPVR	30	15
		874.54	2	NNLEALEDFEKAAGAR	67	84
		934.6	2	YIFYCEGELHGKPVR	14	—
		496.84	2	GELHGKPVR	—	10
		561.36	2	EGELHGKPVR	—	20
		593.88	2	AVLEKTDEPGK	—	28
		641.38	2	CEGELHGKPVR	—	2
		796.48	2	FYCEGELHGKPVR	—	36
		885.5	2	SDEEIQDVSGTWYLK	—	56
		1171.21	2	HHLLASDEEIQDVSGTWYLK	—	102
		857.88	3	SHVKDHYIFYCEGELHGKPVR	—	47
		Total number of peptides			6	12
		Protein score			136	257
Polymeric immunoglobulin receptor	PIGR_HUMAN	703.95	2	VLDSGFREIENK	38	44
		876.04	2	TVTINCPFKTENAQK	11	—
		854.01	2	QSSGENCDVVVNTLGK	78	47
		573.35	2	QGARGGCITLI	—	3
		775.97	2	TINCPFKTENAQK	—	6
		Total number of peptides			3	4
		Protein score			81	63
Lactotransferrin	TRFL_HUMAN	694.94	2	GPQYVAGITNLKK	16	—
		624.37	2	WCAVGEQELR	15	—
		790.48	2	NLLFNDNTECLAR	37	—
		874.03	2	RSVQWCAVSQPEATK	74	—
		630.91	2	GPQYVAGITNLK	—	21
		702.89	2	QWCAVSQPEATK	—	9
		706.93	2	PIQCIQAIAENR	—	62
		841.97	2	CSTSPLLEACEFLR	—	70
		886.06	2	RDSPIQCIQAIAENR	—	6
		953.55	3	SQQSSDPDPNCVDRPVEGYLAVAVVR	—	30
		982.55	2	SASCVPGADKGQFPNLCR	—	56
		Total number of peptides			4	8
		Protein score			77	141
Serum albumin	ALBU_HUMAN	1020.23	2	VFDEFKPLVEEPQNLIK	38	—
		773.99	2	LKECCEKPLLEK	35	—
		Total number of peptides			2	—
		Protein score			46	—
Ig kappa chain C region	IGKC_HUMAN	714.45	3	HKVYACEVTHQGLSSPVTK	—	79
		1071.18	2	HKVYACEVTHQGLSSPVTK	—	34
		Total number of peptides			—	2
		Protein score			—	79
Proline-rich protein 4	PROL4_HUMAN	815.2	2	DRPARHPQEQPLW	43	15
		801.48	2	FPSVSLQEASSFFR	—	84
		537.66	3	PSVSLQEASSFFRR	—	13
		598.38	2	HPPPPPFQNQQRPPR	—	15
		552.68	3	PPPPPFQNQQRPPR	—	27
		Total number of peptides			1	5
		Protein score			43	84
Secretoglobin family 1D member 1	SG1D1_HUMAN	869.57	1	APLEAVAAK	—	24
		572.9	2	FKAPLEAVAAK	—	39
		988.67	2	QALGSEITGFLLAGKPVFK	—	96
		712.8	3	CQALGSEITGFLLAGKPVFK	—	71
		622.86	2	KCVDTMAYEK	—	10
		Total number of peptides			—	5
		Protein score			—	188
Mammaglobin-B	SG2A1_HUMAN	732.95	2	FKQCFLNQSHR	—	45
		969	2	ELLQEFIDSDAAAEAMGK	—	81
		977.54	2	ELLQEFIDSDAAAEAMGK + oxM	—	7
		Total number of peptides			—	3
		Protein score			—	89
Cystatin-S	CYTS_HUMAN	964.05	2	PNLDTCAFHEQPELQK	—	21
		685.74	3	PNLDTCAFHEQPELQKK	—	29
		1135.65	2	SQPNLDTCAFHEQPELQKK	—	6
		986.04	2	QLCSFEIYEVPWEDR	—	67
		Total number of peptides			—	4
		Protein score			—	70