Cell & Tissue Proteome Analysis

ProteiQ is one of the leading full-service providers of cell and tissue global proteome profiling using a next-generation LC-MS proteomics approach

Hippocampus

Mouse

8300

proteins

This project was performed for an academic research group interested in studying the impact of differential therapeutic treatments on the hippocampus proteome of depressed mice.

On average, ProteiQ identified over 8.3k proteins in each hippocampal sample with 90 minutes of LC-MS DIA analysis with 2.9% missing values and a technical coefficient of variation of ~ 11.7% before normalization.

Muscle

Mouse

4700

proteins

A project performed for a therapeutic company involved the study of the impact of differential therapeutic treatments on mouse muscle, combining both proteome and phospho-proteome profiling.

With a 60-minute LC-MS DIA profiling approach, the ProteiQ team identified, on average, over 4.7k proteins in each unenriched sample and 9.8k phosphopeptides after enrichment with 5.9% and 7.5% missing values respectively.

Nasopharyngeal

Swab

4200

proteins

Proteome analysis of nasopharyngeal swabs resulted in  > 4.2k identifications for the study using 60 minutes of LC-MS DIA analysis with a non-linear gradient.

Challenging sampling conditions, impacted technical variability, and the number of missing values per sample lead to > 20% in both cases. ProteiQ addressed all of the challenges in statistical analysis by factoring in batch effects, sampling effects, and the increase in missing identifications.

Liver

Human

6300

proteins

A project in which liver tissue cells were analysed with/without palmitoylated protein enrichment focused on the validation of selective pathway inhibition after treatment.

> 6.3k proteins were identified with 60 minutes of LC-MS DIA analysis – with a missing value of ~ 1% for non-enriched samples before treatment. The number of identifications varied from 0.2k to 2.4k after treatment and enrichment.

HeLa

Cells

4000

proteins

HeLa cells are a common quality reference used in LC-MS proteomics, yet they are also representative of an average number of identifications in wide ranges of other cell types, e.g., MEF, A549, HEPP.

With the current ProteiQ pipeline, around 4k proteins can be identified in 60 minutes of LC-MS DIA analysis; this value can go as high as 6–7k with increased analysis time or with the utilization of ion mobility.

Nasopharyngeal

3500

Swab

Proteome analysis of nasopharyngeal swabs resulted in, on average, > 3.5k identifications per samples using 60 minutes of LC-MS DIA analysis with a non-linear gradient. In the whole study, however, > 4.2k proteins were identified in different patients. Challenging sampling conditions, impacted technical variability, and the number of missing values per sample lead to > 20% in both cases. ProteiQ addressed all of the challenges in statistical analysis by factoring in batch effects, sampling effects, and the increase in missing identifications.

Our Approach

ProteiQ offers state-of-the-art global proteomic profiling and post-translational modification (PTM) analyses through a next-generation LC-MS proteomics approach. This hypothesis and antibody-free quantitative analysis generates reliable protein expression data suitable for a variety of applications in discovery and preclinical research phases.

Multiple Enrichment Options

ProteiQ applies cutting-edge next-generation LC-MS proteomics to global proteome profiling; the golden standard in quantitative protein analysis. Single-shot, one-hour gradient in data-independent mode (MS-DIA) in combination with label-free quantification ensures that we can reliably, reproducibly, and quantitatively identify proteins of interest within complex samples in the vast majority of cases.

Collagen identification

Phosphoenrichment

Phosphorylation plays a key role in many cellular processes. ProteiQ has implemented several affinity-based protocols for enrichment of low abundant phosphoproteins, either directly or on the peptide level.

Close

Collagen identification

Nucleus Extraction

In many cases, protein expression change analysis is required to be performed on a specific subcellular location to infer the underlying biological mechanisms. Nuclear extraction before LC-MS analysis allows for reliable nucleus isolation and more localized subsequent proteome analysis.

Close

Collagen identification

Lysine Acetylome Enrichment

Lysine acetylation participates in diverse biological functions, yet as with other post-translational modifications, the modified proteins are usually very low abundance. ProteiQ offers a single PTM enrichment approach using anti-acetyl lysine antibody beads for global acetylome analysis.

Close

Collagen identification

Collagen identification

We describe a protocol for multiplexed proteomic analysis using neutron-encoded (NeuCode) stable isotope labeling of amino acids in cells (SILAC) or mice (SILAM). This method currently enables simultaneous comparison of up to nine treatment and control proteomes.

Close

Our Solution

State-of-the-Art LC-MS Equipment

ProteiQ utilizes the latest generation of Thermo Fisher Orbitrap mass spectrometers (Exploris and Fusion) coupled to nano- or micro-flow LC systems. For specific project requirements, ion mobility-enabled workflows are available, including the Bruker timsTOF PRO and FAIMS.

AI based Bioinformatics Pipeline

Our in-house developed AI-based bioinformatics pipeline, InfineQ, is suitable for simultaneous quantitative analysis of thousands of samples. High-confidence identification is provided by utilizing an advanced match-between-runs algorithm and PTM localization analysis.

In-house developed

Automatized Sample Preparation

For standardized workflows, our automatic sample preparation using the Tecan Freedom EVO 150 liquid handling robot can process up to 400 samples a day throughput and can be utilized for the analysis of all conventional biological matrices.

Quality & Compliance Control

Multi-stage quality control along all major processing steps (e.g. sample receipt, sample preparation, MS analysis, bioinformatics analysis) has been implemented in our laboratory information management system; it also includes time-stamped step monitoring and the possibility of report generation.

Contact us

Telephone:

+49 (0)30 39771677

Address:

Am Muehlenberg 11, 14476
Potsdam, Germany

Schedule a meeting