The present disclosure provides a method and apparatus for improvements of sample throughput in proteome analysis by mass spectrometry, by combining multiple non-overlapping isoelectric focusing separations. The method for performing an analysis of a plurality of protein samples, comprises: (a) Adding a proteolytic enzyme of a given specificity to a first protein sample to digest proteins to peptides; (b) Separating the peptides obtained in step (a) by isoelectric focusing; (c) Collecting those peptides which have their isoelectric point value within a first isoelectric point range; (d) Adding a proteolytic enzyme of a given specificity to a second protein sample to digest proteins to peptides; (e) Separating the peptides obtained in step (d) by isoelectric focusing; (f) Collecting those peptides which have their isoelectric point value within a second isoelectric point range, where said second isoelectric point range is different and non-overlapping compared to said first isoelectric point range; (g) Combining the peptides collected in steps (c) and (f) into a single sample and subjecting said sample to mass spectrometry analysis; (h) Deconvoluting signals/data obtained from the mass spectrometry analysis by calculating the isoelectric point of each peptide, and assigning a peptide to the first protein sample if its isoelectric point value matches the isoelectric point range selected in step (c) or to the second protein sample if its isoelectric point value matches the isoelectric point range selected in step (f); and (i) Obtaining quantitative information for proteins of each sample according to magnitude of the signal obtained from each peptide.

The present invention relates to a bioinformation processing analysis method for the identification and quantification of O-linked glycopeptide using high resolution mass spectrum. Particularly, according to the bioinformation processing analysis method of the present invention, the quantitative changes of O-linked glycopeptide containing non-informed sugar chains included in various samples can be efficiently and accurately analyzed; the prediction or diagnosis of disease including cancer can be made easy by using a high resolution mass spectrometer; or the investigation of O-linked glycopeptide structure of a therapeutic glycoprotein can be efficiently achieved.

The present invention provides a method for monitoring esophageal adenocarcinoma (EAC) disease progression in a subject, the method comprising: obtaining a biological sample from the subject; measuring with a quantitative analytical method at least one metabolite; determining a metabolomic biosignature of EAC disease progression based on a comparison of quantitative data for the at least one metabolite to corresponding data obtained for at least one reference sample; and identifying active EAC disease progression in the subject if the quantity of the at least one metabolite in the sample from the subject is greater than that found in the at least one reference sample.

The invention provides for methods for isolating large EVs and detecting palmitoyl proteins in the large EVs, as well as methods for detecting clinically significant prostate cancer based on the presence of palmitoyl proteins in the isolated large EVs in a subject in need thereof. The method further comprises administering cancer therapy to the subject.

A method of capturing human immunoglobulin Fc domains in a biofluid sample is provided. The method includes providing an affinity capture device. The affinity capture device includes a surface having an aptamer that is at least 80% identical to SEQ ID NO 1 immobilized onto the surface of the affinity capture device. The biofluid sample is diluted with a binding buffer. The binding buffer includes (A) tris(hydroxymethyl)aminomethane (Tris), trimethylamine (TES), 2-ethanesulfonic acid (MES), or 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES); (B) a magnesium cation at a concentration between about 10 M to about 20 mM; and (C) a total monovalent cation concentration from 0 to no greater than 100 mM. The human immunoglobulin Fc domains in the biofluid sample are adsorbed to the aptamer with the binding buffer.

A method for identifying neoantigens that are likely to be presented by MHC alleles on a surface of tumor cells of a subject. Peptide sequences of the tumor neoantigens and of the MHC alleles are obtained by sequencing the tumor cells of the subject. The peptide sequences of the tumor neoantigens and of the MHC alleles are input into a machine-learned presentation model to generate presentation likelihoods for the tumor neoantigens, each presentation likelihood representing the likelihood that a neoantigen is presented by at least one of the MHC alleles on the surface of the tumor cells of the subject. A subset of the neoantigens is selected based on the presentation likelihoods.

Provided herein are proteomic biomarkers of spontaneous preterm birth, proteomic biomarkers of term birth, and methods of use thereof. In particular, provided are tools for determining whether a pregnant subject is at an increased risk for premature delivery, as well as tools for decreasing a pregnant subject's risk for premature delivery.

Disclosed is a method of preparing a sample that is suitably used for analysis of a glycoprotein or glycopeptide. A first reaction is performed to modify or remove at least one primary amino group contained in a peptide moiety of a glycopeptide or glycoprotein. Thereafter, a second reaction is performed. The second reaction is a reaction capable of modifying a carboxy group of sialic acid of a sugar chain. After the second reaction, a derivative from 2,3-linked sialic acid a derivative from 2,6-linked sialic acid have different masses. Determination of the presence or absence of sialic acid in the sugar chain of a glycoprotein or glycopeptide and identification of the linkage type of sialic acid can be simply performed by mass spectrometry.

The present invention is directed to a mass spectrometry approach to identifying non-Spitzoid melanoma, and distinguishing non-Spitzoid nevi from non-Spitzoid malignant melanoma.

The invention provides methods for characterizing a target protein wherein a mass spectrum of digest peptides of the target protein is acquired and compared with measured reference mass spectra of digest peptides of reference proteins or of proteins of reference host cells. The comparison comprises determining similarity scores of the intensity patterns of the mass spectrum and the reference mass spectra. The characterization comprises assigning the target protein to a reference protein having a reference mass spectrum with a similarity score above a predetermined threshold.