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

Band Namea	Protein name	Protein accession	Mass (Da)	Mascot scoreb	No. of matched  sequencesb	No. of peptide  sequencesb	Sequence coverageb (%)	Peptide sequences confirmed by MS/MS
a	Heat shock protein HSP-90 beta	HS90_HUMANf	83242	134	8	7	13	IDIIPNPQERGVVDSEDLPLNISR
b	Trifunctional enzyme subunit alpha, mitochondrial	ECHA_HUMAN	82947	127	21	16	28	TLQEVTQLSQEAQRTVLGTPEVLLGALPGAGGTQR
	6-phosphofructokinase, platelet type	K6PP_HUMAN	85542	118	24	19	31	YLEEIATQMRAIGVLTSGGDAQGMNAAVR
c	ATP synthase subunit alpha, mitochondrial	ATPA_HUMAN	59714	128	10	9	26	EAYPGDVFYLHSRTGAIVDVPVGEELLGREVAAFAQFGSDLDAATQQLLSR
	Tubulin beta-5 chainc	TBB5_HUMANf	49640	261	26	21	61	FPGQLNADLRAILVDLEPGTMDSVRISEQFTAMFR
	Tubulin alpha-1C chaind	TBA1C_HUMANf	49863	163	18	16	47	AVFVDLEPTVIDEVR
d	Sulfide quinone oxidoreductase, mitochondrial	SQRD_HUMAN	49929	188	22	19	49	IMYLSEAYFRIMYLSEAYFR+Oxid(M)YADALQEIIQER GYWGGPAFLR
e	Actin, cytoplasmice	ACTB_HUMANf	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	LFDQAFGLPRLATQSNEITIPVTFESR

^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.