Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

The preset invention relates to a high resolution mass spectrometry based novel bioinformatics platform for the identification of glycation proteins and advanced glycation end-product. Particularly, the bioinformatics platform of the present invention facilitates an efficient and accurate investigation of quantitative changes of glycation proteins and advanced glycation end-products which are included in various types of samples but had not been informed yet, and uses a high resolution mass spectrometry, and thereby can be effectively used for the prediction or diagnosis of a disease including cancer by examining a disease marker in a sample.

A processing platform in one embodiment comprises one or more processing devices each including at least one processor coupled to a memory. The processing platform is configured to implement a crosslink identification and validation algorithm for processing multiple levels of mass spectrometry data in order to identify and validate protein-protein interactions within the mass spectrometry data. In conjunction with execution of the crosslink identification and validation algorithm, the processing platform is further configured to obtain mass spectrometry spectra for each of the multiple levels, to apply a header matching filter to identify at least one potential crosslink relating one or more first level spectra and one or more second level spectra utilizing a plurality of third level spectra, and to apply one or more mass validation filters to identify whether or not the potential crosslink is a valid crosslink.

Method and devices are provided for imaging a surface, such as a biological tissue sample, by mass spectrometry. In certain aspects, devices of the embodiments allow for the placement and collection of a plurality of spatially separated liquid droplets on a sample and delivery of the droplets with extracted sample analytes for mass spectrometry analysis.

Methods are provided for determining the amount of an IGF-I and/or IGF-II protein in a sample using high resolution / high accuracy mass spectrometry. The methods generally comprise enriching an IGF-I and/or IGF-II protein in a sample, ionizing an IGF-I and/or IGF-II protein from the sample to generate IGF-I and/or IGF-II protein ions, and determining the amount of IGF-I and/or IGF-II protein ions with high resolution / high accuracy mass spectrometry.

Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

This disclosure provides quantitative, rapid, and reliable LC-MS/MS methods for analyzing panels of pesticides and mycotoxins in various samples, including very hydrophobic and chlorinated compounds normally analyzed on a GC-MS/MS system. The methods can be carried out using a single instrument and can detect and quantify levels of the pesticides and mycotoxins that are well below action limits specified by U.S. states (e.g., California) and other countries (e.g., Canada) for these compounds in cannabis products.

The disclosure features methods of identifying protein-protein deregulation that include: generating a basal protein-protein interaction network for a plurality of biological samples, the network featuring a set of proteins expressed in the biological samples and concentrations of each member of the set of expressed proteins in each of the biological samples; identifying two associated expressed proteins in the network; for the two associated expressed proteins, comparing correlated relative concentration values of the two proteins in each of the biological samples to identify outliers among a distribution of the relative concentration values; and identifying members of the plurality of biological samples in which deregulation of the two associated expressed proteins occurs based on the outliers.

Provided herein are methods for identifying new biomarkers for various diseases using proteomics, peptidomics, metabolics, proteoglycomics, glvcomics, mass spectrometry and machine learning. The present disclosure also provides glycopeptides as biomarkers for various diseases such as cancer and autoimmune diseases.

The present invention relates to a method for determining the quality of haemoglobin (Hb) during the storage period of red blood cell (RBC) units comprising a step of detecting soluble alpha-haemoglobin (α-Hb) pool in RBC lysates and concluding that the presence of α-Hb pool indicates a conservation of quality of Hb during the storage RBCs. Inventors have determined the impact of RBC units aging on the quality of Hb and on the soluble α-Hb pool level in RBCs. For this purpose, 21 RBC units were collected, stored at +4 to 6° C. and samples were taken at two different storage times (D3-D8 and D38-D42) to evaluate spectral characteristics of Hb and soluble α-Hb pool in RBCs. Two additional samples were collected from 16 RBC units, at intermediate time points during storage (D13-D17 and D24-D29; n=16). The α-Hb dosing assay uses the specific character of the interaction between the α-Hb and the AHSP, the α chaperone, to trap the α-Hb present in the RBC lysates of RBC units. They also investigated the effect of a short cryopreservation period at −80° C. for 15 days on the α-Hb pool for 4 different RBC units.