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Open Access Method

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

Zia Khan123, Sasan Amini245, Joshua S Bloom24, Cristian Ruse6, Amy A Caudy27, Leonid Kruglyak289, Mona Singh12, David H Perlman1024 and Saeed Tavazoie1124*

Author Affiliations

1 Department of Computer Science, Washington Rd, Princeton University, Princeton, NJ 08544, USA

2 Lewis-Sigler Institute for Integrative Genomics Washington Rd, Princeton University, Princeton, NJ 08544, USA

3 Current address: Department of Human Genetics, South Ellis Avenue, University of Chicago, Chicago, IL 60637, USA

4 Department of Molecular Biology, Washington Rd, Princeton University, Princeton, NJ 08544, USA

5 Current address: Illumina Inc., Towne Centre Drive, San Diego, CA 92121, USA

6 Cold Spring Harbor Laboratory, Bungtown Rd, Cold Spring Harbor, NY 11724, USA

7 Current address: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, King's College Circle, Toronto, Ontario, M5S 1A1, Canada

8 Department of Ecology and Evolutionary Biology, Washington Rd, Princeton University, Princeton, NJ 08544, USA

9 Howard Hughes Medical Institute, Washington Rd, Princeton University, Princeton, NJ 08544, USA

10 Princeton Mass Spectrometry Center, Washington Rd, Princeton University, Princeton, NJ 08544, USA

11 Current address: Department of Biochemistry and Molecular Biophysics, 116th Street and Broadway, Columbia University, New York, NY 10027, USA

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Genome Biology 2011, 12:R122  doi:10.1186/gb-2011-12-12-r122

Published: 19 December 2011

Additional files

Additional file 1:

Supplementary figures. Additional figures referred to in the text.

Format: PDF Size: 1.7MB Download file

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Additional file 2:

Peptide ratios for fractionated data set. Raw peptide ratios reported by our method for the solubility and SCX fractionated E. coli protein samples.

Format: XLS Size: 12.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Sensitivity and specificity results. False discovery rate (FDR) 1% score thresholds and total number of quantified peptides with and without our method for limiting peptides scored during MS/MS database search based on nitrogen composition applied to a data set.

Format: XLS Size: 11KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data