Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

doi:10.1186/1477-5956-7-22

Proteome Science

Volume 7

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Kuntumalla S
Braisted JC
Huang ST
Parmar PP
Clark DJ
Alami H
Zhang Q
Donohue-Rolfe A
Tzipori S
Fleischmann RD
Peterson SN
Pieper R

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Kuntumalla S
Braisted JC
Huang ST
Parmar PP
Clark DJ
Alami H
Zhang Q
Donohue-Rolfe A
Tzipori S
Fleischmann RD
Peterson SN
Pieper R
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Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

Srilatha Kuntumalla¹ , John C Braisted¹ , Shih-Ting Huang¹ , Prashanth P Parmar¹ , David J Clark¹ , Hamid Alami¹ , Quanshun Zhang² , Arthur Donohue-Rolfe² , Saul Tzipori² , Robert D Fleischmann¹ , Scott N Peterson¹ and Rembert Pieper¹

¹Pathogen Functional Genomics Resource Center, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

²Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, North Grafton, MA 01536, USA

author email corresponding author email

Proteome Science 2009, 7:22doi:10.1186/1477-5956-7-22


Published:	29 June 2009

Additional files

Additional file 1:

Additional Table S1. Correlation of APEX estimates of a ten protein standard mixture with known protein concentrations ranging from 1 – 500 pmol (R_s= 0.98, R²= 0.92).

Format: XLS Size: 956KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Additional Table S2. Protein abundance estimates from 2-DE spot intensity quantitation. 271 proteins are listed with 2D gel spot numbers, accession numbers, gene names, locus tags, protein description, abundance values, physicochemical properties and subcellular localizations. 16 proteins unique to the 2D gel analysis are in bold letters.

Format: XLS Size: 602KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Additional Table S3. Protein abundance estimates from APEX quantitation. 1148 proteins are listed with the false positive error rate, p_i, n_i, O_iand APEX abundance values calculated using the APEX Quantitative Proteomics Tool. The corresponding gene names, locus tags, physicochemical properties and subcellular localizations are also listed in the table.

Format: XLS Size: 1016KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

Additional Table S4. Comparison of SD1 protein abundance estimates from APEX vs. 2-DE quantitations for 255 common proteins listed along with 2D gel spot numbers, gene names, locus tags, physicochemical properties and subcellular localizations.

Format: XLS Size: 559KB Download file

This file can be viewed with: Microsoft Excel Viewer