Table 1.

Example: matching the M. genitalium spot G18 peptide mass fingerprint data with protein B64230 in the database

Start-End	Observed m/z	Mr (expt)	Mr (calc)	Delta mass(Da)	Modification	Missed cleavages	Database sequence	Peptide sequence ion score
4–22	2157.10	2156.09	2156.09	-0.00	Oxidation (M)	0	K.IQVNNIEALNNAMDLALER.D	25
23–41	2070.99	2069.98	2069.98	0.00		0	R.DQNVVLYGQDAGFEGGVFR.A	105
109–118	1074.65	1073.65	1073.62	0.02		0	R.GVYTAPLVVR.M	37
147–157	1268.59	1267.59	1267.58	0.01	Oxidation (M)	0	K.TVMPSNPYDTK.G	-
158–176	2090.11	2089.11	2089.11	-0.01		0	K.GLFLAAIESPDPVIFFEPK.K	-
158–177	2298.19	2297.19	2297.17	0.01	Phospho (ST)	1	K.GLFLAAIESPDPVIFFEPKK.L	-
230–239	1171.69	1170.69	1170.66	0.03		1	K.DKGIELIDLR.T	-
232–239	928.57	927.56	927.54	0.02		0	K.GIELIDLR.T	45
247–254	922.51	921.51	921.49	0.01		0	K.QTVFNSVK.K	-
259–267	971.63	970.62	970.61	0.01		0	R.LLVVTEAVK.S	42
294–305	1286.77	1285.76	1285.74	0.02		0	R.VTGFDIVVPLAR.G	72
309–316	1040.54	1039.53	1039.51	0.02		0	K.YQFEINAR.V	52
317–326	1112.68	1111.67	1111.66	0.01		0	R.VIDAVNQLLK.-	41

The peptide profile of spot G18, treated with trypsin and analyzed by MALDI-TOF-TOF. Mascot was used for the database search with MSDB version 20050227. 13/45 peptides were matched to B64230, pyruvate dehydrogenase E1-beta chain. The peptide sequence ion score corresponds to peptides analyzed and identified by MS/MS sequencing, and peptides without a score (-) were detected only in the MS data. Ion scores of 20 or greater are significant. The matched peptide sequences are shown by underline in the sequence below.

1   MSKIQVNNIEALNNAMDLALERDQNVVLYGQDAGFEGGVFRATKGLQQKY GSERVWDCPI AENSMAGIGV GAAIGGLKPI VEIQFSGFSF PAMFQIFVHA

101 ARIRNRSRGVYTAPLVVRMP MGGGIKALEH HSETLEAIYA QIAGLKTVMPSNPYDTKGLFLAAIESPDPVIFFEPKKLYR AFRQEIPSDY YTVPIGEANL

201 ISEGSELTIV SYGPTMFDLI NLVYSGELKDKGIELIDLRT ISPWDKQTVFNSVKKTGRLLVVTEAVKSFT TSAEIITSVT EELFTYLKKA PQRVTGFDIV

301 VPLARGEKYQFEINARVIDAVNQLLK