We describe here an on-line combination of a surface acoustic wave (SAW) biosensor with electrospray ionization mass spectrometry (SAW-ESI-MS) that enables the direct detection, identification, and quantification of affinity-bound ligands from a protein-ligand complex on a biosensor chip. A trapping column was used between the SAW-biosensor and the electrospray mass spectrometer equipped with a micro-guard column, which provides simultaneous sample concentration and desalting for the mass spectrometric analysis of the dissociated ligand. First applications of the on-line SAW-ESI-MS combination include (1), differentiation of ␤-amyloid (A␤) epitope peptides bound to anti-A␤ antibodies; (2), the identification of immobilized Substance P peptide-calmodulin complex; (3), identification and quantification of the interaction of 3-nitrotyrosine-modified peptides with nitrotyrosine-specific antibodies; and (4), identification of immobilized anti-␣-synuclein-human ␣-synuclein complex. Quantitative determinations of protein-ligand complexes by SAW yielded dissociation constants (K D ) from micro-to low nanomolar sample concentrations. The on-line bioaffinity-ESI-MS combination presented here is expected to enable broad bioanalytical application to the simultaneous, label-free determination and quantification of biopolymer-ligand interactions, as diverse as antigen-antibody and lectin-carbohydrate complexes. (J Am Soc Mass Spectrom 2010, 21, 1643-1648 [3,4]. In particular, SPR has developed into an efficient tool for analysis of biomolecular recognition processes at a biosensor surface, and has been applied to the quantification of a variety of biopolymer interactions [4,5]. A recently-explored alternative to SPR is the surface acoustic wave (SAW) technology in which the piezoelectric effect of mass differences is employed for bioaffinity detection [6 -9]. SAW is now becoming increasingly important for the study of biomacromolecular interactions due to its high detection sensitivity in dilute solutions.Advantages of SAW in comparison to classical immuno-analytical techniques are the direct and rapid determination of association/dissociation constants with small sample amounts, and without labeling approaches or recalibration for buffer changes being required [6]. While providing sensitive and accurate determinations of binding/dissociation constants (K i or K D ), a major limitation of all bioaffinity methods is the lack of direct identification of the affinity-bound ligands. In contrast, the combination of biosensor detection and mass spectrometry enables both identification and quantification of bioaffinity interactions of biopolymers. Here we describe an on-line combination of an SAW biosensor with electrospray ionization mass spectrometry, SAW-ESI-MS. The on-line coupling between the SAW-sensor chip and the ESI-MS source was achieved by a incorporating a standard trapping column setup, using a six-port valve, a guard column, and a micropump system. The six-port valve interface provides both ligand concentration and an...

Nitration of tyrosine residues has been shown to be an important oxidative modification in proteins and has been suggested to play a role in several diseases such as atherosclerosis, asthma, lung and neurodegenerative diseases. Detection of nitrated proteins has been mainly based on the use of nitrotyrosine-specific antibodies. In contrast, only a small number of nitration sites in proteins have been unequivocally identified by MS. We have used a monoclonal 3-NT-specific antibody, and have synthesized a series of tyrosine-nitrated peptides of prostacyclin synthase (PCS) in which a single specific nitration site at Tyr-430 had been previously identified upon reaction with peroxynitrite17. The determination of antibody-binding affinity and specificity of PCS peptides nitrated at different tyrosine residues (Tyr-430, Tyr-421, Tyr-83) and sequence mutations around the nitration sites provided the identification of an epitope motif containing positively charged amino acids (Lys and/or Arg) N-terminal to the nitration site. The highest affinity to the anti-3NT-antibody was found for the PCS peptide comprising the Tyr-430 nitration site with a K(D) of 60 nM determined for the peptide, PCS(424-436-Tyr-430NO(2) ); in contrast, PCS peptides nitrated at Tyr-421 and Tyr-83 had substantially lower affinity. ELISA, SAW bioaffinity, proteolytic digestion of antibody-bound peptides and affinity-MS analysis revealed highest affinity to the antibody for tyrosine-nitrated peptides that contained positively charged amino acids in the N-terminal sequence to the nitration site. Remarkably, similar N-terminal sequences of tyrosine-nitration sites have been recently identified in nitrated physiological proteins, such as eosinophil peroxidase and eosinophil-cationic protein.

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 2 AbstractThe stoichiometries and the affinity toward simple and paired metal ions of synthetic amyloid-β(1-40)peptide (Aβ1-40) were investigated by electrospray ion trap mass spectrometry (ESI-MS), circular dichroism (CD), and atomic force microscopy (AFM). The results lead to the working hypothesis that pHdependent metal binding to Aβ1-40 may induce conformational changes, which affect the affinity toward other metals. A significant copper and zinc binding to Aβ1-40 peptide at pH 5.5 was found, whereas nickel ions commonly bind to each molecule of β-amyloid peptide. Some complexes of Aβ1-40 with more than one nickel ion were identified by ESI-MS. In addition, nickel ions proved to enhance Aβ oligomerization. On increasing pH, up to 12 ions of zinc may bind to a single Aβ molecule. Under the same pH and concentration conditions, the binding pattern of the independent copper and silver ions to Aβ1-40 was different from that of the equimolecular mixture of the two metal ions. One might assume that some conformational changes due to water loss altered the capacity of Aβ peptide to bind certain heavy metal ions. As a consequence, copper-silver interaction with the binding process to Aβ1-40 became highly complex. A competition between silver and nickel ions for Aβ1-40 binding sites at high pH was also observed. New strategies were proposed to identify the characteristic signals for some important metal ion-peptide complexes in the spectra recorded at high pH or high concentrations of metal ions. To explain the formation of such a large number of high metal ion-Aβ complexes, we took into consideration the participation of both histidine residues and free amino groups as well as carboxylate ones in the binding process. Finally, CD and AFM studies supported the mass spectrometric data.

A new methodology using hydrogen/deuterium amide exchange (HDX) to determine the binding affinity of protein-peptide interactions is reported. The method, based on our previously established approach, protein ligand interaction by mass spectrometry, titration, and H/D exchange (PLIMSTEX) [J. Am. Chem. Soc. 2003, 125, 5252-5253], makes use of a dilution strategy (dPLIMSTEX) for HDX, using the mass of the peptide ligand as readout. We employed dPLIMSTEX to study the interaction of calcium-saturated calmodulin with the opioid peptide ␤-endorphin as a model system; the affinity results are in good agreement with those from traditional PLIMSTEX and with literature values obtained by using other methods. We show that the dPLIMSTEX method is feasible to quantify an antigen-antibody interaction involving a 3-nitrotyrosine modified peptide in complex with a monoclonal anti-nitrotyrosine antibody. A dissociation constant in the low nanomolar range was determined, and a binding stoichiometry of antibody/peptide of 1:2 was confirmed. In addition, we determined that the epitope in the binding interface contains a minimum of five amino acids. The dPLIMSTEX approach is a sensitive and powerful tool for the quantitative determination of peptide affinities with antibodies, complementary to conventional immuno-analytical techniques. (J Am Soc Mass

Nitration of tyrosine residues in proteins has been mainly characterised by immunoanalytical methods using anti-3-nitrotyrosine antibodies, and nitration sites and sequences have been hitherto identified only in a few cases using mass spectrometric methods. Immuno-analytical methods frequently suffer from low and poorly characterised detection specificity of antinitrotyrosine antibodies, while mass spectrometric methods for identification of Tyrosine nitration may be hampered by low levels of modification, and by possible changes of structure and proteolytic degradation of proteins introduced by the nitration. Moreover, no detailed, molecular characterisation of the specificity of anti-3-nitrotyrosine antibodies has been reported. In this study we describe a molecular study of the recognition specificities and affinities of two commercially available, monoclonal anti-nitrotyrosine antibodies by affinity-mass spectrometry, using different 3-nitrotyrosine containing peptides. Tyrosine-nitrated and non-nitrated substrate peptides of prostacyclin synthase (PCS), an enzyme inactivated by nitration of the active site Tyr-430 residue, were synthesised by solid-phase peptide synthesis (SPPS), purified by reversed phasehigh performance liquid chromatography (RP-HPLC) and characterised by electrospray (ESI) and matrix-assisted laser desorption-ionisation (MALDI) mass spectrometry. Binding affinities and specificities of PCS peptides with different Tyr-nitration sites and sequence mutations adjacent to Tyr-430 were determined by evaluation of anti-nitrotyrosine antibodies using an affinitymass spectrometry approach, compared to immuno-analytical determination using dot-blot and ELISA. The results showed that the antibodies may discriminate in the recognition of peptides with different N-terminal adjacent sequences to the nitrotyrosine residues, depending on the type of immunogen employed. A quantitative ELISA estimation was developed for the determination of antibody binding by Tyrosine-nitrated peptides.