Abstract: MRM triggered MRM, where the triggered MRM transitions make use of mobility device parameter values for the same compound, is performed. A plurality of primary MRM transitions are received and stored together with a mobility device parameter value for each transition as an MRM cycle list. Control information instructs a mobility device and a mass spectrometer to interrogate each MRM transition on the MRM cycle list within an MRM cycle of the mass spectrometer. If a product ion intensity value of an MRM transition exceeds a threshold value for a primary MRM transition, a plurality of secondary MRM transitions of the primary MRM transition with different mobility device parameter values are added to the MRM cycle list. The intensities of the measured secondary MRM transitions provide information on the optimum mobility device parameter for each compound.

Abstract: MRM triggered MRM, where the triggered MRM transitions make use of mobility device parameter values for the same compound, is performed. A plurality of primary MRM transitions are received and stored together with a mobility device parameter value for each transition as an MRM cycle list. Control information instructs a mobility device and a mass spectrometer to interrogate each MRM transition on the MRM cycle list within an MRM cycle of the mass spectrometer. If a product ion intensity value of an MRM transition exceeds a threshold value for a primary MRM transition, a plurality of secondary MRM transitions of the primary MRM transition with different mobility device parameter values are added to the MRM cycle list. The intensities of the measured secondary MRM transitions provide information on the optimum mobility device parameter for each compound.

Abstract: Computer-implementable methods consistent with the present teachings can be used in the design of selective- and multiple-reaction monitoring experiments for the identification of proteins and peptides of interest. By determining candidate parent-daughter ion transition pairs and scoring the pairs based on their ability to be detected experimental design time can be reduced and with a more focused list of transition pairs more experiments can be run successfully in a given period of time.

Abstract: The present teachings provide methods for the development of a mass spectrometric based assay for a protein in a sample using parent-daughter ion transition monitoring (PDITM). In various aspects, the present teachings provide methods for developing a mass spectrometric based assay for a protein in a sample without the use of a standard for the protein. In various embodiments, the sample comprises proteolytic fragments of a protein which is present in low abundance in the physiological fluid from which it is derived.

Abstract: The present teachings provide methods for the development of a mass spectrometric based assay for a protein in a sample using parent-daughter ion transition monitoring (PDITM). In various aspects, the present teachings provide methods for developing a mass spectrometric based assay for a protein in a sample without the use of a standard for the protein. In various embodiments, the sample comprises proteolytic fragments of a protein which is present in low abundance in the physiological fluid from which it is derived.

Abstract: The present invention relates to methods and compositions for lipid matrix-assisted chemical ligation and synthesis of membrane polypeptides that are incorporated in a lipid matrix. The invention is exemplified in production of a prefolded membrane polypeptide embedded within a lipid matrix via stepwise chemoselective chemical ligation of unprotected peptide segments, where at least one peptide segment is embedded in a lipid matrix. Any chemoselective reaction chemistry amenable for ligation of unprotected peptide segments can be employed. Suitable lipid matrices include liposomes, micelles, cell membrane patches and optically isotropic cubic lipidic phase matrices. Prefolded synthetic and semi-synthetic membrane polypeptides synthesized according to the methods and compositions of the invention also permit site-specific incorporation of one or more detectable moieties, such as a chromophore, which can be conveniently introduced during synthesis.

Abstract: In various aspects, the present teachings provide systems, methods, assays and kits for the absolute quantitation of protein expression. In various aspects, the present teachings provide methods of determining the concentration of about the top forty-one proteins present in human plasma. In various aspects, the present teachings provide methods of determining the absolute concentration of one or more proteins using standard samples of signature protein fragments and parent-daughter ion transition monitoring (PDITM). In various embodiments, the absolute concentration of multiple isoforms of a biomolecule in a sample, multiple proteins in a biological process, a combination of multiple samples, or combinations thereof, can be determined in a multiplex fashion using the present teachings. In various aspects, provided are methods of assessing the state of a biological system including, but not limited to, the disease state of an animal.

Abstract: The present invention relates to methods and compositions for modifying peptides, polypeptides and proteins with polymers, especially glyco-mimetic polymers, so as to improve their biological activity or pharmacokinetic properties. The invention further provides methods and uses for such polymer-modified peptides, polypeptides and proteins. The invention is particularly suitable for use in the synthesis of polymer-modified synthetic bioactive proteins (FIG. 1D), and of pharmaceutical compositions that contain such proteins.

Abstract: The present invention concerns methods and compositions for extending the technique of native chemical ligation of a wider range of peptides, polypeptides, other polymers and other molecules via an amide bond (see FIG. 1). The invention further provides methods and uses for such proteins and derivatized proteins. The invention is particularly suitable for use in the synthesis of optionally polymer-modified, synthetic bioactive proteins, and of pharmaceutical compositions that contain such proteins.

Abstract: The present invention relates to methods and compositions for modifying peptides, polypeptides and proteins with polymers, especially glyco-mimetic polymers, so as to improve their biological activity or pharmacokinetic properties. The invention further provides methods and uses for such polymer-modified peptides, polypeptides and proteins. The invention is particularly suitable for use in the synthesis of polymer-modified synthetic bioactive proteins (FIG. 1D), and of pharmaceutical compositions that contain such proteins.

Abstract: The present invention concerns methods and compositions for extending the technique of native chemical ligation of a wider range of peptides, polypeptides, other polymers and other molecules via an amide bond (see FIG. 1). The invention further provides methods and uses for such proteins and derivatized proteins. The invention is particularly suitable for use in the synthesis of optionally polymer-modified, synthetic bioactive proteins, and of pharmaceutical compositions that contain such proteins.

Abstract: The present invention relates to methods and compositions for lipid matrix-assisted chemical ligation and synthesis of membrane polypeptides that are incorporated in a lipid matrix. The invention is exemplified in production of a prefolded membrane polypeptide embedded within a lipid matrix via stepwise chemoselective chemical ligation of unprotected peptide segments, where at least one peptide segment is embedded in a lipid matrix. Any chemoselective reaction chemistry amenable for ligation of unprotected peptide segments can be employed. Suitable lipid matrices include liposomes, micelles, cell membrane patches and optically isotropic cubic lipidic phase matrices. Prefolded synthetic and semi-synthetic membrane polypeptides synthesized according to the methods and compositions of the invention also permit site-specific incorporation of one or more detectable moieties, such as a chromophore, which can be conveniently introduced during synthesis.

Abstract: The present invention relates to methods and compositions for lipid matrix-assisted chemical ligation and synthesis of membrane polypeptides that are incorporated in a lipid matrix. The invention is exemplified in production of a prefolded membrane polypeptide embedded within a lipid matrix via stepwise chemoselective chemical ligation of unprotected peptide segments, where at least one peptide segment is embedded in a lipid matrix. Any chemoselective reaction chemistry amenable for ligation of unprotected peptide segments can be employed. Suitable lipid matrices include liposomes, micelles, cell membrane patches and optically isotropic cubic lipidic phase matrices. Prefolded synthetic and semi-synthetic membrane polypeptides synthesized according to the methods and compositions of the invention also permit site-specific incorporation of one or more detectable moieties, such as a chromophore, which can be conveniently introduced during synthesis.