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Table 1 Differentially expressed proteins in S. Typhimurium exposed to pSWCNT-Ag

From: Proteomic analysis of antimicrobial effects of pegylated silver coated carbon nanotubes in Salmonella enterica serovar Typhimurium

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

  1. 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
  2. bSubcellular localization was predicted using pSORTb version 3.0
  3. cPredicted molecular weight (MW) and d isoelectric point (pI)
  4. 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)
  5. 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)
  6. 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