Provided herein are methods of preparing a protein sample for proteomic analysis. In exemplary embodiments, the method comprises (a) contacting a blood sample comprising proteins with a protective agent comprising an anticoagulant (AC) and an aldehyde releaser (AR), to obtain a mixture, optionally, wherein the blood sample is added to a blood collection tube (BCT) comprising the protective agent, and (b) isolating a fraction comprising proteins or a source of proteins from the mixture to yield a protein sample or a source of a protein sample, wherein steps of the method are carried out in the absence of exogenous proteolytic enzyme inhibitors, wherein the protein sample is suitable for proteomic analysis. Preferably, the protective agent consists of essentially (i) about 300 g/l to about 700 g/l imidazolidinyl urea; (ii) about 20 g/l to about 60 g/l glycine; and (iii) about 60 g/l to about 100 g/l EDTA; and the protein sample is analysed via mass spectrometry-based proteomic methods.

Useful, accessible, and predictive biomarkers for discriminating between ovarian cancer and benign adnexal masses are provided. Specifically, peptide biomarkers present in bodily fluid samples such as cervical-vaginal fluid (CVF) have been identified as having particularly robust diagnostic for identifying whether ovarian masses such as adnexal masses are benign, and ruling our ovarian cancer. The biomarker peptides disclosed herein therefore provide significantly enhanced sensitivity and specificity levels relative to extant methods for distinguishing benign ovarian masses from ovarian cancers. The biomarkers provide a timely and cost-efficient diagnostic capable of being used in a selection process to identify patients for whom treatment, which may include surgical resection and/or monitoring, may be performed by an obstetric gynecologist rather than a gynecologic oncologist.

The present disclosure provides an improved method for profiling the nature of undesirable host cell proteins (HCPs) in a therapeutic antibody preparation using an improved assay. The assay includes three (3) exemplary steps comprising: ultra-low trypsin digestion, long gradient liquid chromatography, and mass spectrometry (MS) using, in particular, BoxCar mass spectrometry. The disclosure allows for determining the purity of a therapeutic antibody such that it is suitable for use in patients.

Provided is a display-processing device for mass spectrometry data capable of presenting a mass spectrum of a test microorganism and existing genome-related information so that the relationship between the two kinds of information can be easily understood. In the device, a spectrum acquirer (41) acquires a mass spectrum (80) of a test microorganism. A genome-related information acquirer (42) acquires genome-related information of a known microorganism which is identical or related to the test microorganism, based on the mass spectrum. A correspondence relationship determiner (43) determines a correspondence relationship between peaks on the mass spectrum and proteins expressed in the known microorganism. A display controller (45) displays, on a display device, identifiers (81) and a genome map (70) along with the mass spectrum, each identifier indicating what protein corresponds to a given peak, and the genome map showing the location of the gene encoding each protein on the genome.

Disclosed is a method for identifying methicillin-resistant Staphylococcus aureus through detection a mass signal at m/z of 6580-6600 in the MALDI-TOF mass spectrum. Also disclosed is a novel peptide biomarker, which consists of SEQ NO ID:5 and the use thereof for detection and/or identification of methicillin-resistant Staphylococcus aureus.

Methods for achieving complete sequence coverage of monoclonal antibodies by trypsin digestion and dual-column LC-MS system are provided. The disclosed method improves upon current techniques for standard peptide mapping.

An example binding assay includes a plurality of sub-regions, a plurality of synthetic compounds on beads, wherein each of the plurality of sub-regions includes one of the plurality of synthetic compounds, a biological target labeled with a first detectable label in each of the plurality sub-regions, and a biological counter target labeled with a second detectable label in each of the plurality of sub-regions. The biological counter target is configured to bind to the biological target when the biological target is in a first orientation. And, wherein a first subset of the plurality of synthetic compounds bind to the biological target and effect interactions between the biological target and the biological counter target.

The disclosure relates to a system comprising software that predicts responsiveness of subjects to certain disease modifying drugs. Embodiments of the disclosure include methods comprising calculating a differential interaction score (DIS), correlating the DIS with the likelihood that a dysfunctional protein-protein interaction is the causal agent of a disease or disorder, and identifying a subject responsive to a treatment based upon the causal agent.

Various embodiments of the present disclosure relate to a method for analyzing target compounds from a fluid or dried biological sample by using a microfluidic sample device including a hollow cartridge and an absorbent body unit.

A system and method for using new biomarkers to assess individual diseases is provided. In one embodiment of the present invention, absolute quantification of annotated metabolites by mass spectrometry is used to identify certain biomarkers and derivatives thereof (i.e., signatures), which are then used to screen for, diagnose, predict, prognose, and treat various diseases, including, but not limited to, breast cancer, ovarian cancer, colorectal cancer, pancreatic cancer, and acute graft-versus-host disease.