Table 1.

Differentially expressed proteins in S. Typhimurium exposed to pSWCNT-Ag

Spot ID	Protein name	NCBI no.	Abbr.	Func.a	Local.b	MW (kDa)c	pId	No. of peptide matched	Protein scoree	Total ion scoref	Protein score CI %g	Total ion CI %h
Down-regulated
2506	Flagellin FliC	gi|446001950	hag	N	Extracellular	51.5	4.79	16	930	830	100	100
3603 3605 4601	Aspartate ammonia-lyase	gi|445991585	aspA	E	Cytoplasmic	52.2	5.15	17	450	335	100	100
4405	Outer membrane protein A	gi|487406894	ompA	M	Outer membrane	37.4	5.6	16	571	449	100	100
4508	Adenylosuccinate synthetase	gi|446450117	purA	F	Cytoplasmic	47.3	5.31	21	265	116	100	100
5503 5508	arginine deiminase	gi|446332991	STM4467	E	Cytoplasmic	45.5	5.47	22	774	586	100	100
5401	Ornithine carbamoyltransferase	gi|446159176	STM4465	E	Cytoplasmic	36.7	5.28	11	585	514	100	100
5408	Carbamate kinase	gi|446350896	STM4466	E	Cytoplasmic	33.3	5.45	13	399	307	100	100
6406	l-Asparaginase 2	gi|446316334	ansB	E	Periplasmic	36.9	5.84	13	347	262	100	100
8003	Universal stress protein F	gi|447005040	uspF	J	Unknown	15.7	5.93	11	406	296	100	100
9001	Ethanolamine utilization protein EutM	gi|446309861	eutM	E	Unknown	9.8	6.06	6	164	110	100	100
Up-regulated
2101	Outer membrane protease	gi|446639417	ompX	M	Outer membrane	18.4	5.74	9	500	425	100	100
2204 3202	Alkyl hydroperoxide reductase subunit C	gi|445974947	ahpC	V	Cytoplasmic	20.7	5.03	10	437	354	100	100
5303	Propanediol utilization microcompartment protein PduB	gi|446019642	pduB	Q	Unknown	27.9	5.21	9	378	318	100	100
7105	DNA starvation/stationary phase protection protein	gi|446022950	dps	J	Cytoplasmic	18.7	5.73	14	476	336	100	100
8401	Aldehyde dehydrogenase	gi|446075650	gapA	C	Cytoplasmic	35.5	6.33	20	572	393	100	100

^aFunctional classification was performed using COGs (Clusters of Orthologous Groups) functional annotation. C energy production and conversion, E amino acid transport and metabolism, F nucleotide transport and metabolism, J translation, ribosomal structure and biogenesis, M cell wall/membrane/envelope biogenesis, N cell motility, Q secondary metabolites biosynthesis, transport and catabolism, V defense mechanisms

^bSubcellular localization was predicted using pSORTb version 3.0

^cPredicted molecular weight (MW) and ^d isoelectric point (pI)

^eProtein scores are derived from ion scores as a non-probabilistic basis for the ranking protein hits. Ions score is − 10 log(P), where P is the probability that the observed peptide match is a random event (http://www.matrixscience.com/help/interpretation_help.html)

^fTotal ion score is calculated by weighting ion scores for all individual peptides matched to the protein that is associated with this peptide and MS/MS spectrum (http://www.matrixscience.com/help/interpretation_help.html)

^gConfidence interval % (CI %) rates the confidence level of the protein score [MS] or ion score [MS/MS]. The CI % is the statistical calculation based on the distribution of the probability that enables to compare the searched data base with the number of submitted mass spectra for the database searches