Table 1 Proteins identified by MALDI-TOF-MS in gel bands of PtpA D126A substrate trapping assays

Band Name^a	Protein name	Protein accession	Mass (Da)	Mascot score^b	No. of matched sequences^b	No. of peptide sequences^b	Sequence coverage^b (%)	Peptide sequences confirmed by MS/MS
a	Heat shock protein HSP-90 beta	HS90_HUMAN^f	83242	134	8	7	13	IDIIPNPQER GVVDSEDLPLNISR
b	Trifunctional enzyme subunit alpha, mitochondrial	ECHA_HUMAN	82947	127	21	16	28	TLQEVTQLSQEAQR TVLGTPEVLLGALPGAGGTQR
	6-phosphofructokinase, platelet type	K6PP_HUMAN	85542	118	24	19	31	YLEEIATQMR AIGVLTSGGDAQGMNAAVR
c	ATP synthase subunit alpha, mitochondrial	ATPA_HUMAN	59714	128	10	9	26	EAYPGDVFYLHSR TGAIVDVPVGEELLGR EVAAFAQFGSDLDAATQQLLSR
	Tubulin beta-5 chain^c	TBB5_HUMAN^f	49640	261	26	21	61	FPGQLNADLR AILVDLEPGTMDSVR ISEQFTAMFR
	Tubulin alpha-1C chain^d	TBA1C_HUMAN^f	49863	163	18	16	47	AVFVDLEPTVIDEVR
d	Sulfide quinone oxidoreductase, mitochondrial	SQRD_HUMAN	49929	188	22	19	49	IMYLSEAYFR IMYLSEAYFR+Oxid(M) YADALQEIIQER GYWGGPAFLR
e	Actin, cytoplasmic^e	ACTB_HUMAN^f	41710	82	4	4	15	SYELPDGQVITIGNER
f	Phosphate carrier protein, mitochondrial	MPCP_HUMAN	39933	76	7	6	18	IQTQPGYANTLR
g	Cytochome C1, mitochondrial	CY1_HUMAN	35399	77	3	2	9	AANNGALPPDLSYIVR+Deamidated NQ
h	Heat Shock protein beta 1	HSPB1_HUMAN	22768	167	5	5	29	LFDQAFGLPR LATQSNEITIPVTFESR

^aBand name corresponds to the gel pieces indicated in the SDS-PAGE shown in Fig. 3.
^bFor each protein the value of score, number of matched and peptide sequences indicated is the best value obtained from two biological replicates.
^cTBB3_HUMAN, TBB2A_HUMAN and TBB4B_HUMAN were also identified with the same set of peptides.
^dTBA1A_HUMAN, TBA1B_HUMAN were also identified with the same set of peptides.
^eACTG_HUMAN was also identified with the same set of peptides.
^fProteins identified in mock substrate trapping using the more sensitive approach of Nano LC-MS.

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