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ANIBAL, stable isotope-based quantitative proteomics by aniline and benzoic acid labeling of amino and carboxylic groups

Panchaud, Alexandre; Hansson, Jenny LU ; Affolter, Michael; Bel Rhlid, Rachid; Piu, Stéphane; Moreillon, Philippe and Kussmann, Martin (2008) In Molecular & Cellular Proteomics 7(4). p.12-800
Abstract

Identification and relative quantification of hundreds to thousands of proteins within complex biological samples have become realistic with the emergence of stable isotope labeling in combination with high throughput mass spectrometry. However, all current chemical approaches target a single amino acid functionality (most often lysine or cysteine) despite the fact that addressing two or more amino acid side chains would drastically increase quantifiable information as shown by in silico analysis in this study. Although the combination of existing approaches, e.g. ICAT with isotope-coded protein labeling, is analytically feasible, it implies high costs, and the combined application of two different chemistries (kits) may not be... (More)

Identification and relative quantification of hundreds to thousands of proteins within complex biological samples have become realistic with the emergence of stable isotope labeling in combination with high throughput mass spectrometry. However, all current chemical approaches target a single amino acid functionality (most often lysine or cysteine) despite the fact that addressing two or more amino acid side chains would drastically increase quantifiable information as shown by in silico analysis in this study. Although the combination of existing approaches, e.g. ICAT with isotope-coded protein labeling, is analytically feasible, it implies high costs, and the combined application of two different chemistries (kits) may not be straightforward. Therefore, we describe here the development and validation of a new stable isotope-based quantitative proteomics approach, termed aniline benzoic acid labeling (ANIBAL), using a twin chemistry approach targeting two frequent amino acid functionalities, the carboxylic and amino groups. Two simple and inexpensive reagents, aniline and benzoic acid, in their (12)C and (13)C form with convenient mass peak spacing (6 Da) and without chromatographic discrimination or modification in fragmentation behavior, are used to modify carboxylic and amino groups at the protein level, resulting in an identical peptide bond-linked benzoyl modification for both reactions. The ANIBAL chemistry is simple and straightforward and is the first method that uses a (13)C-reagent for a general stable isotope labeling approach of carboxylic groups. In silico as well as in vitro analyses clearly revealed the increase in available quantifiable information using such a twin approach. ANIBAL was validated by means of model peptides and proteins with regard to the quality of the chemistry as well as the ionization behavior of the derivatized peptides. A milk fraction was used for dynamic range assessment of protein quantification, and a bacterial lysate was used for the evaluation of relative protein quantification in a complex sample in two different biological states.

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Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
keywords
Amino Acid Sequence, Amino Acids, Aniline Compounds, Animals, Bacterial Proteins, Benzoic Acid, Carbon Isotopes, Cattle, Computational Biology, Humans, Isotope Labeling, Milk Proteins, Milk, Human, Molecular Sequence Data, Peptides, Proteomics, Serum Albumin, Bovine
in
Molecular & Cellular Proteomics
volume
7
issue
4
pages
13 pages
publisher
American Society for Biochemistry and Molecular Biology
external identifiers
  • Scopus:42649098635
ISSN
1535-9484
DOI
10.1074/mcp.M700216-MCP200
language
English
LU publication?
no
id
64b2e965-a0b2-4e0f-acb0-982f03b5b351
date added to LUP
2016-08-25 09:56:43
date last changed
2016-10-13 05:12:46
@misc{64b2e965-a0b2-4e0f-acb0-982f03b5b351,
  abstract     = {<p>Identification and relative quantification of hundreds to thousands of proteins within complex biological samples have become realistic with the emergence of stable isotope labeling in combination with high throughput mass spectrometry. However, all current chemical approaches target a single amino acid functionality (most often lysine or cysteine) despite the fact that addressing two or more amino acid side chains would drastically increase quantifiable information as shown by in silico analysis in this study. Although the combination of existing approaches, e.g. ICAT with isotope-coded protein labeling, is analytically feasible, it implies high costs, and the combined application of two different chemistries (kits) may not be straightforward. Therefore, we describe here the development and validation of a new stable isotope-based quantitative proteomics approach, termed aniline benzoic acid labeling (ANIBAL), using a twin chemistry approach targeting two frequent amino acid functionalities, the carboxylic and amino groups. Two simple and inexpensive reagents, aniline and benzoic acid, in their (12)C and (13)C form with convenient mass peak spacing (6 Da) and without chromatographic discrimination or modification in fragmentation behavior, are used to modify carboxylic and amino groups at the protein level, resulting in an identical peptide bond-linked benzoyl modification for both reactions. The ANIBAL chemistry is simple and straightforward and is the first method that uses a (13)C-reagent for a general stable isotope labeling approach of carboxylic groups. In silico as well as in vitro analyses clearly revealed the increase in available quantifiable information using such a twin approach. ANIBAL was validated by means of model peptides and proteins with regard to the quality of the chemistry as well as the ionization behavior of the derivatized peptides. A milk fraction was used for dynamic range assessment of protein quantification, and a bacterial lysate was used for the evaluation of relative protein quantification in a complex sample in two different biological states.</p>},
  author       = {Panchaud, Alexandre and Hansson, Jenny and Affolter, Michael and Bel Rhlid, Rachid and Piu, Stéphane and Moreillon, Philippe and Kussmann, Martin},
  issn         = {1535-9484},
  keyword      = {Amino Acid Sequence,Amino Acids,Aniline Compounds,Animals,Bacterial Proteins,Benzoic Acid,Carbon Isotopes,Cattle,Computational Biology,Humans,Isotope Labeling,Milk Proteins,Milk, Human,Molecular Sequence Data,Peptides,Proteomics,Serum Albumin, Bovine},
  language     = {eng},
  number       = {4},
  pages        = {12--800},
  publisher    = {ARRAY(0xa191820)},
  series       = {Molecular & Cellular Proteomics},
  title        = {ANIBAL, stable isotope-based quantitative proteomics by aniline and benzoic acid labeling of amino and carboxylic groups},
  url          = {http://dx.doi.org/10.1074/mcp.M700216-MCP200},
  volume       = {7},
  year         = {2008},
}