Current chemical tagging strategies for proteome analysis by mass spectrometry

Leitner, Alexander; Lindner, Wolfgang

doi:10.1016/j.jchromb.2004.09.057

Cited by 107 publications

(84 citation statements)

References 213 publications

(321 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Affinity chromatography has grown rapidly as a complementary method for multidimensional separations in proteomics [3,13]. Specifically for the enrichment of L-DOPA-containing peptides, a boronic acid phase effectively operating at pH < 7 would be desirable in order to avoid adventitious oxidation of the analytes on column.…”

Section: Introductionmentioning

confidence: 99%

Synthesis of sulfonamide- and sulfonyl-phenylboronic acid-modified silica phases for boronate affinity chromatography at physiological pH

Pennington

Stobaugh

et al. 2008

Analytical Biochemistry

View full text Add to dashboard Cite

Two new types of boronate affinity solid phases were synthesized and characterized. The materials were prepared by silylation of porous silica gel with monochlorosilane derivatives containing synthetic sulfonyl-and sulfonamide-substituted phenylboronic acids. The new solid phases were evaluated for boronate affinity chromatography with aryl and alkyl cis-diol compounds, and found suitable for the retention of cis-diols under acidic conditions. Significant correlations between the retention factor (K) and the pH of the mobile phase demonstrate that the binding of cis-diols to the solid phases is best rationalized by chelation. Based on the low ionization constant, caused by the electron-withdrawing effects of the sulfonyl and sulfonamide groups, these media display an enhanced affinity for cis-diols as compared to unsubstituted phenylboronic acid. Utilizing Isocratic elution, a mixture of various biologically relevant L-tyrosines, L-DOPA and several catecholamines were resolved with a mobile phase composed of 0.05 M, pH5.5 phosphate buffer. Mono-, di-and triphosphates of adenosine were also separated at pH 6.0. Hence, the new boronate solid phase offers efficient affinity separation and purification of cis-diol containg molecules under rather mild pH regions.

show abstract

Section: Introductionmentioning

confidence: 99%

Synthesis of sulfonamide- and sulfonyl-phenylboronic acid-modified silica phases for boronate affinity chromatography at physiological pH

Pennington

Stobaugh

et al. 2008

Analytical Biochemistry

View full text Add to dashboard Cite

show abstract

“…These complications were recently addressed by our group (33,34). We further note that although pairs of related spectra can also be identified by chemical tagging procedures (44,45) or special instrumentation (46), these approaches do not consider overlapping peptides and cannot match spectra from multiple samples. Fig.…”

Section: Methodsmentioning

confidence: 99%

Shotgun Protein Sequencing

Bandeira

Clauser

Pevzner

2007

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

Despite significant advances in the identification of known proteins, the analysis of unknown proteins by MS/MS still remains a challenging open problem. Although Klaus Biemann recognized the potential of MS/MS for sequencing of unknown proteins in the 1980s, low throughput Edman degradation followed by cloning still remains the main method to sequence unknown proteins. The automated interpretation of MS/MS spectra has been limited by a focus on individual spectra and has not capitalized on the information contained in spectra of overlapping peptides. Indeed the powerful shotgun DNA sequencing strategies have not been extended to automated protein sequencing. We demonstrate, for the first time, the feasibility of automated shotgun protein sequencing of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities. We validate this approach by generating highly accurate de novo reconstructions of multiple regions of various proteins in western diamondback rattlesnake venom. We further argue that shotgun protein sequencing has the potential to overcome the limitations of current protein sequencing approaches and thus catalyze the otherwise impractical applications of proteomics methodologies in studies of unknown proteins. Molecular & Cellular Proteomics 6:1123-1134, 2007.Current approaches to proteomics focus on the reliable identification of proteins under the assumption that all proteins of interest are known and present in a database. However, the limited availability of sequenced genomes and multiple mechanisms of protein variation often refute this assumption. Well known mechanisms of protein diversity include variable recombination and somatic hypermutation of immunoglobulin genes (1). The vital importance of some of these novel proteins is directly reflected in the success of monoclonal antibody drugs such as Rituxan TM , Herceptin TM , and Avastin TM (2, 3), all derived from proteins that are not directly inscribed in any genome. Similarly multiple commercial drugs have been developed from proteins obtained from species whose genomes are not known. In particular, peptides and proteins isolated from venom have provided essential clues for drug design (4, 5); examples include drugs for controlling blood coagulation (6 -8) and drugs for breast (9, 10) and ovarian (11) cancer treatment. Even so, the genomes of the venomous snakes, scorpions, and snails are unlikely to become available anytime soon.Despite this vital importance of novel proteins, the mainstream method for protein sequencing is still initiated by restrictive and low throughput Edman degradation (12, 13), a task made difficult by protein purification procedures, posttranslational modifications, and blocked protein N termini. These problems gain additional relevance when one considers the unusually high level of variability and post-translational modifications in venom proteins (14,15). Moreover the common labor-intensive approach of DNA cloning and sequencing...

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%

“…This is so certainly because of its universal applicability to any kind of biological sample (cells, tissues, or biological fluids) including ex vivo sampling from higher organisms and because of the wide range of available quantification targets, i.e. 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

Current chemical tagging strategies for proteome analysis by mass spectrometry

Cited by 107 publications

References 213 publications

Synthesis of sulfonamide- and sulfonyl-phenylboronic acid-modified silica phases for boronate affinity chromatography at physiological pH

Synthesis of sulfonamide- and sulfonyl-phenylboronic acid-modified silica phases for boronate affinity chromatography at physiological pH

Shotgun Protein Sequencing

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

Contact Info

Product

Resources

About