An Isotope Coding Strategy for Proteomics Involving Both Amine and Carboxyl Group Labeling

Liu, Peiran; Regnier, Fred E.

doi:10.1021/pr0255304

Cited by 47 publications

(39 citation statements)

References 22 publications

(87 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The effect of this is the same as if the purity of the H 2 18 O used for labeling were lower. Various efforts have been made to drive the reaction further toward complete incorporation of two 18 O atoms (11,28,29). Increasing the concentration of trypsin in the labeling reaction will also increase the reaction rate.…”

Section: Resultsmentioning

confidence: 99%

A Method for Automatically Interpreting Mass Spectra of 18O-Labeled Isotopic Clusters

Mason

Therneau

Eckel‐Passow

et al. 2007

Molecular & Cellular Proteomics

114

View full text Add to dashboard Cite

O. The algorithm operates on centroided peak lists and is therefore very fast: nine chromatograms of, on average, 1,168 spectra and containing, on average, 6,761 isotopic clusters were interpreted in, on average, 45 s per chromatogram. RAAMS is fast enough (average, 38 ms/ spectrum) to allow the possibility of performing informationdependent MS/MS on a chromatographic time scale on species exceeding predetermined ratio thresholds. We describe in detail the operation of the algorithm and demonstrate its use on datasets with known and unknown ratios. Molecular & Cellular Proteomics 6:305-318, 2007.

show abstract

Section: Resultsmentioning

confidence: 99%

A Method for Automatically Interpreting Mass Spectra of 18O-Labeled Isotopic Clusters

Mason

Therneau

Eckel‐Passow

et al. 2007

Molecular & Cellular Proteomics

114

View full text Add to dashboard Cite

show abstract

“…The advantage of stable isotope-based methods relies on their efficiency when coupled to MS. As a consequence, several strategies have been developed based on stable, non-radioactive isotopes like 2 H, 13 C, 15 N, and 18 O and can be classified in three stable isotope labeling experiment categories: (i) metabolic stable isotope labeling like stable isotope labeling by amino acids in cell culture (SILAC) using growth medium with stable isotopelabeled amino acids (6) or via isotope-labeled nutrients like [ 15 N]ammonium salt (7,8); (ii) isotope tagging by chemical reaction such as ICAT, isotope-coded protein labeling (ICPL), or isobaric tagging for relative and absolute quantification (iTRAQ) (5,9,10); and (iii) enzyme-catalyzed reactions like 16 O/ 18 O exchange in terminal carboxylic groups conferred by trypsin or other proteases (11,12). Typically two biological conditions (control versus case) are defined and compared with regard to their protein expression profile.…”

mentioning

confidence: 99%

“…amino acids amenable to derivatization (Cys, Lys, Met, Trp, His, Asp, Glu, or N/C termini) (15)(16)(17). Almost all approaches are based on a single labeling, but Liu and Regnier (18) described for the first time a strategy using a dual chemistry targeting amino and carboxylic groups at the peptide level.…”

mentioning

confidence: 99%

ANIBAL, Stable Isotope-based Quantitative Proteomics by Aniline and Benzoic Acid Labeling of Amino and Carboxylic Groups

Panchaud

Hansson

Affolter

et al. 2008

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

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 Creagent 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. Molecular & Cellular Proteomics 7:800 -812, 2008.

show abstract

“…The first major application of this strategy involved the derivatization of cysteine residues with isotopic variants of the ICAT, a reagent composed of an affinity tag (biotin) separated by a polyether linker from the reactive moiety [8,9]. Alternative postdigestion isotopic labeling techniques include selective derivatization of carboxylic acids [10] and primary amines [11][12][13]. However, these chemical reactions suffer from the large number of reaction sites present in the macromolecule.…”

mentioning

confidence: 99%

Relative quantification of tau-related peptides using guanidino-labeling derivatization (GLaD) with online-LC on a hybrid ion trap (IT) time-of-flight (ToF) mass spectrometer

Bereszczak

Brancia

Quijano

et al. 2007

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Development of a quantification method based on isotopic variants of O-methyl isourea (OMIU) in conjunction with reversed-phase (RP) liquid chromatography (LC) electrospray mass spectrometry is described for determining the relative quantification of -related peptides Ac-VQIVXK-NH 2 . Extracted ion chromatograms of the mass spectrometric data derived from online microcapillary LC separation identifies the retention times of the isotopically derivatized peptides together with their ion abundances. Data-dependent MSMS analysis of both derivatized variants of the same peptide provides a complementary method for identification and resolution between isobaric species. In addition, with respect to offline LC MALDI a larger number of analogues are detected and formation of amyloid is also observed for the aspartic acid and histidine-containing peptides. (J Am Soc Mass Spectrom 2007, 18, 201-207) © 2007 American Society for Mass Spectrometry D efining cellular dynamics in terms of changes in protein expression levels means it is no longer sufficient to simply qualitatively identify proteins; instead, methods for protein quantification are required. Relative protein quantification relies largely on the use of differential stable isotope labeling [1,2]. This strategy can be achieved in vivo, by metabolic labeling of proteins by cell growth in the presence of isotopically labeled amino acids [3], or in vitro by chemical derivatization of the proteins or their corresponding proteolysis products. In both cases the proteins or peptides that are to be compared are labeled separately with isotopic variants of a specific compound. The mixtures containing isotopically derivatized peptides are then recombined before mass spectrometric (MS) analysis. Relative quantification is determined by the ratio of the ion abundances of the two derivatized peptide ions under comparison. In vivo metabolic labeling involves the growth of a given cell population in a medium containing the natural form of an essential amino acid, whereas the other cell population is grown in a medium containing the heavy isotopic variant of this amino acid, such as leucine versus deuterated leucine (Leu-d 3 ) [4,5] or arginine versus deuterated arginine ( 13 C 6 -Arg) [6,7]. A number of methods have been developed for the selective derivatization of functional groups within proteins/peptides using isotopic variants of a given chemical reagent. The first major application of this strategy involved the derivatization of cysteine residues with isotopic variants of the ICAT, a reagent composed of an affinity tag (biotin) separated by a polyether linker from the reactive moiety [8,9]. Alternative postdigestion isotopic labeling techniques include selective derivatization of carboxylic acids [10] and primary amines [11][12][13]. However, these chemical reactions suffer from the large number of reaction sites present in the macromolecule. A far easier reaction to control is the guanidination of lysine residues based on the use of O-methyl isourea (OMIU) [14 -17]. Develop...

show abstract

An Isotope Coding Strategy for Proteomics Involving Both Amine and Carboxyl Group Labeling

Cited by 47 publications

References 22 publications

A Method for Automatically Interpreting Mass Spectra of 18O-Labeled Isotopic Clusters

A Method for Automatically Interpreting Mass Spectra of 18O-Labeled Isotopic Clusters

ANIBAL, Stable Isotope-based Quantitative Proteomics by Aniline and Benzoic Acid Labeling of Amino and Carboxylic Groups

Relative quantification of tau-related peptides using guanidino-labeling derivatization (GLaD) with online-LC on a hybrid ion trap (IT) time-of-flight (ToF) mass spectrometer

Contact Info

Product

Resources

About