Abstract: Methods for analyzing, selecting, characterizing or classifying compositions of a co-polymer, e.g., glatiramer acetate are described. The methods entail analysis of pyro-glutamate in the composition, and, in some methods, comparing the amount of pyro-glutamate present in a composition to a reference standard.

Abstract: Methods for analyzing, selecting, characterizing or classifying compositions of a co-polymer, e.g., glatiramer acetate are described. The methods entail analysis of pyro-glutamate in the composition, and, in some methods, comparing the amount of pyro-glutamate present in a composition to a reference standard.

Abstract: Accordingly, systems and methods for protein identification are provided. The present teaching provide for a system with one protein identification methodology based on one method and a second protein identification methodology based on a second protein identification methodology to interact and increase confidence in protein identification. Various embodiments employ protein identification methodologies that identify portions of a peptide. Various embodiments provide for a hypothesis generation module that can suggest modifications for the peptide based on differences between experimental and theoretical values. Various embodiments provide for an identifier module that can select one or more hypotheses from the hypothesis module as most probable. In this way, the present teachings can provide for systems and methods to combine protein identification results from multiple protein identification methodologies with the possibility of identifying modifications.

Abstract: The present disclosure provides methods for assessing the glycosylation of a target glycoprotein produced by a cell through analysis of cell-surface glycans on the cell. The present disclosure therefore teaches that glycosylation of cell surface proteins can serve as a proxy for glycosylation of other proteins.

Abstract: The present disclosure provides, among other things, methods for the identification of sulfated glycans in a mixture of glycans.

Abstract: In various aspects, provided are methods for identification of the presence of modified peptides using at least in part mass spectrometric signals from metastable ions that are formed in the field free region of the analyzer. For example, in various embodiments where the modified peptides are phosphopeptides, such metastable ions can appear approximately 95 u lower than the precursor ion m/z value from which they were formed when the peptide contains a phosphate group. In various embodiments, detection of such metastable ions in a MALDI-TOF mass spectrum can identify the modified peptide. In various aspects, provided are methods for identification of the presence of modified peptides using at least in part MS/MS data from two or more of modified peptides, de-modified peptides and non-modified peptides by comparing the sequence and/or site of modification information for two or more of these three forms of a peptide.

Abstract: Methods for analyzing, selecting, characterizing or classifying compositions of a co-polymer, e.g., glatiramer acetate are described. The methods entail analysis of pyro-glutamate in the composition, and, in some methods, comparing the amount of pyro-glutamate present in a composition to a reference standard. In some cases, the methods entail treating the co-polymer with pyro-glutamate aminopeptidase to cleave N-terminal pyro-glutamate residues.

Abstract: Accordingly, systems and methods for protein identification are provided. The present teaching provide for a system with one protein identification methodology based on one method and a second protein identification methodology based on a second protein identification methodology to interact and increase confidence in protein identification. Various embodiments employ protein identification methodologies that identify portions of a peptide. Various embodiments provide for a hypothesis generation module that can suggest modifications for the peptide based on differences between experimental and theoretical values. Various embodiments provide for an identifier module that can select one or more hypotheses from the hypothesis module as most probable. In this way, the present teachings can provide for systems and methods to combine protein identification results from multiple protein identification methodologies with the possibility of identifying modifications.

Abstract: In various aspects, provided are methods for identification of the presence of modified peptides using at least in part mass spectrometric signals from metastable ions that are formed in the field free region of the analyzer. For example, in various embodiments where the modified peptides are phosphopeptides, such metastable ions can appear approximately 95 u lower than the precursor ion m/z value from which they were formed when the peptide contains a phosphate group. In various embodiments, detection of such metastable ions in a MALDI-TOF mass spectrum can identify the modified peptide. In various aspects, provided are methods for identification of the presence of modified peptides using at least in part MS/MS data from two or more of modified peptides, de-modified peptides and non-modified peptides by comparing the sequence and/or site of modification information for two or more of these three forms of a peptide.

Abstract: A matrix for mass spectrometry, the matrix comprising an additive that minimizes or eliminates adduct formation and/or chemical noise generation is disclosed. Also disclosed is a method for depositing a matrix on a MALDI target plate and a disposable plate having a dissolvable pre-matrix deposited thereon. The matrix material can be 2,5-dimethoxybenzoic acid and a monobasic or dibasic salt or tribasic salt as an adduct-reducing additive, such as ammonium monobasic phosphate and sulfate salts, dibasic citrate salts and tribasic citrate salts.