OMICS
OMICS
Protocol
IsoCode Single-Cell Adaptive Immune: Human CAR-T Protocol Using AF647-Conjugated Antibodies to CD4 and CD8
Overview of ProtocolDay 1: Cryopreserved CAR-T cells are thawed and cultured overnight in the presence of IL-2. Cryopreserved target cell lines are thawed, cultured, and passaged several days prior to beginning the experiment.Day 2: Enrichment and Antigen-Stimulation of CD8 + and/or CD4 + CAR-T cell... More
Protocol
Rapid and sensitive label-free proteome quantification on the timsTOF Pro 2
Shotgun proteomics capacity to deliver in-depth information on the identification, the relative amount, and the modification patterns of ever larger fraction of the proteins present in a sample has made it an essential approach in most biological research areas. The recent introduction of Parallel A... More
Protocol
Ultra-high sensitivity proteomics on the timsTOF SCP
The timsTOF Pro platform, introduced in 2017, already featured a sensitivity boost from the Parallel Accumulation SErial Fragmentation (PASEF) technology, which provides time and space focusing of the ions in the Trapped Ion Mobility Spectrometry (TIMS) tunnel. The timsTOF SCP platform further enhan... More
Protocol
MRMS powered single cell metabolomics – Quantification of picogram amounts of a biocatalytic product from few living cells
Probing the metabolic state of living microbial cells via their secreted metabolic products is highly challenging as it requires measures to maintain the cellular integrity and to collect the analytes. This application note demonstrates how direct infusion magnetic resonance mass spectrometry (DI-MR... More
Protocol
prm-PASEF®: enabling high-throughput, high sensitivity targeted proteomics
In comparison with standard selected and parallel reaction monitoring (SRM and PRM), the prm-PASEF increases the number of peptides that can be targeted in a single acquisition method, without compromising the selectivity or the sensitivity. Using a prototype acquisition software, we targeted 201 is... More
Protocol
Incorporating CCS values to enable 4-dimensional annotation of metabolic features
Reliable annotation of metabolites for LC-MS/MS based data requires the adept combination of many parameters such as retention time and accurate mass. To extend our parameter portfolio, we analyzed the high reproducible measured CCS values using trapped ion mobility spectrometry (TIMS) to provide ad... More
Protocol
Studying protein-drug complexes under native conditions in the low nM range using MRMS
Protein ligand complexes need to be preserved through the electrospray and detection process. This work describes high resolution native mass spectrometric measurements of the enzyme carbonic anhydrase II (Figure 1) and the non-covalent complex with the substrate acetazolamide (Figure 2) using a sci... More
Protocol
Proteomic Interrogation of Primary Insulin-secreting Pancreatic β-cells
In this work we leveraged the analytical performance of the timsTOF Pro to identify expression of low-level enzymes for the first time in primary insulinsecreting beta cells (β-cells). We found that these proteins are critical, functional components of key metabolic pathways which can support β-cell... More
Protocol
Magnetic Resonance Mass Spectrometry (MRMS) discriminates yeast mutants through metabolomics
A eukaryote model of Saccharomyces cerevisiae was used to study the methylglyoxal pathway by Magnetic resonance mass spectrometry (MRMS). It was discovered that glutathione plays a major role in driving metabolomic differences between different strains. It is expected that metabolomics-based discrim... More
Protocol
Elucidation of metabolic changes in HFD-ApoE–/– model by SP6 peptide: A flow injection analysis magnetic resonance mass spectrometry (FIA-MRMS) study
The employment of natural peptides in the treatment of cardiovascular diseases is an attractive option to pharmacological therapy. In this study, a novel antihypertensive peptide from Spirulina Platensis (SP6) was employed to evaluate its potential anti-atherosclerotic effect in high fat diet ApoE–/... More
Protocol
A Protocol for Qualifying DNA Variants Associated with Complex Diseases like Ehlers-Danlos syndrome
A protocol for DNA variant qualification adds medical perspective to consensus grading based on impact of the DNA change on its encoded RNA/protein and its prevalence in normal people versus those with the implicated disease. This clinically familiar 1-4+ qualification can encourage physician accept... More
Protocol
MALDI Guided SpatialOMx uncovers proteomic profiles in tumor subpopulations of breast cancer
The timsTOF fleX system bridges a current gap by providing MALDI Imaging and in-depth proteomics analysis in just one instrument. The instrument offers all benefits of a timsTOF Pro for timeefficient and sensitive proteomics, combined with a high-resolution MALDI source and stage. Using PASEF techno... More
Protocol
CodePlex Secretome
This protocol outlines the standard method for thawing and loading samples onto the CodePlex chip. ... More
Protocol
IsoCode Single-Cell Adaptive Immune: Human CAR-T Protocol Using AF647-Conjugated Antibodies to CD4 and CD8
Overview of ProtocolDay 1: Cryopreserved CAR-T cells are thawed and cultured overnight in the presence of IL-2. Cryopreserved target cell lines are thawed, cultured, and passaged several days prior to beginning the experiment.Day 2: Enrichment and Antigen-Stimulation of CD8 + and/or CD4 + CAR-T cell... More
Protocol
Rapid and sensitive label-free proteome quantification on the timsTOF Pro 2
Shotgun proteomics capacity to deliver in-depth information on the identification, the relative amount, and the modification patterns of ever larger fraction of the proteins present in a sample has made it an essential approach in most biological research areas. The recent introduction of Parallel A... More
Protocol
Ultra-high sensitivity proteomics on the timsTOF SCP
The timsTOF Pro platform, introduced in 2017, already featured a sensitivity boost from the Parallel Accumulation SErial Fragmentation (PASEF) technology, which provides time and space focusing of the ions in the Trapped Ion Mobility Spectrometry (TIMS) tunnel. The timsTOF SCP platform further enhan... More
Protocol
MRMS powered single cell metabolomics – Quantification of picogram amounts of a biocatalytic product from few living cells
Probing the metabolic state of living microbial cells via their secreted metabolic products is highly challenging as it requires measures to maintain the cellular integrity and to collect the analytes. This application note demonstrates how direct infusion magnetic resonance mass spectrometry (DI-MR... More
Protocol
prm-PASEF®: enabling high-throughput, high sensitivity targeted proteomics
In comparison with standard selected and parallel reaction monitoring (SRM and PRM), the prm-PASEF increases the number of peptides that can be targeted in a single acquisition method, without compromising the selectivity or the sensitivity. Using a prototype acquisition software, we targeted 201 is... More
Protocol
Incorporating CCS values to enable 4-dimensional annotation of metabolic features
Reliable annotation of metabolites for LC-MS/MS based data requires the adept combination of many parameters such as retention time and accurate mass. To extend our parameter portfolio, we analyzed the high reproducible measured CCS values using trapped ion mobility spectrometry (TIMS) to provide ad... More
Protocol
Studying protein-drug complexes under native conditions in the low nM range using MRMS
Protein ligand complexes need to be preserved through the electrospray and detection process. This work describes high resolution native mass spectrometric measurements of the enzyme carbonic anhydrase II (Figure 1) and the non-covalent complex with the substrate acetazolamide (Figure 2) using a sci... More
Application
Access the Breadth of Sample Preparation Protocols to Awaken True Functional Immune Biology
Precedent Protocols and Processes ensure that enrichment, stimulation and labeling will result in maximizing the correlative data achieved, while minimizing non-specific impact on the cells themselves. Highlights: • Published enrichment, stimulation, and staining protocols throughout immunotherapy ... More
Primer
Source and Elimination of Common Mass Spectrometry Contaminants
Sensitivity is a key attribute of mass spectrometers to allow quantification of minute amounts of analytes. Yet this sensitivity can be a conundrum. Myriad sources can contribute contaminants that can impact background and confound interpretation of results. An increased background signal can make i... More
Primer
Selecting a Functional Oligonucleotide from a Random Mix
SELEX (Systematic Evolution of Ligands by EXponential enrichment) was first described and used in 1990 to isolate a functional oligonucleotide from a random pool of differently-shaped DNA or RNA molecules.1-2SELEX-derived oligonucleotides (RNA or single-stranded DNA) known as aptamers, bind with hig... More
Primer
Single-Cell RNA Sequencing Upgrades Sensitivity
A new method for DNA amplification and sequencing called TAS-Seq improves the accuracy of single-cell RNA sequencing (scRNA-seq). TAS-Seq uses a terminal transferase enzyme that amplifies and sequences DNA complementary to mRNA (cDNA) in solid phase on a nanowell/magnetic bead-based cell isolation p... More
Primer
Cyclic Microchip Assay Enhances Throughput of Protein Detection in Single Cells
Most existing single-cell protein analysis methods can analyze about a dozen proteins at a time when the execution of nearly every conceivable cellular function depends on a complex and diverse proteome.A new microchip assay called CycMIST1 (single-cell cyclic multiplex in situ tagging) can measure ... More
Primer
Solvent Precipitation Method Increases Protein Recovery for Proteomics
Study designs in proteomics aim for inclusivity—to characterize every protein in a sample. However, extracting proteins from complex biological samples involves the use of harsh buffers containing detergents and salts that are incompatible with the proteomics workflow. More proteins are lost in atte... More
Mixer
Mapping Tissue Carbohydrates Using Mass Spectrometry
This mixer will be relevant for all interested in methods used in glycoproteomics research that aims to understand the pivotal role of carbohydrate motifs that modify the proteome.Glycoproteomics, a dynamic area of frontier research, provides a systems biology approach to understanding the biologica... More
Mixer
Spatial Biology Tools and Techniques
Single-cell spatial phenotyping is transforming biomedical research in fields ranging from oncology to neuroscience. This GEN Protocols Mixer focuses on technological developments and protocols that have enabled spatial approaches in biology. We will explore novel applications of the technology in d... More