Collaborators across the proteomics ecosystem

Flexible workflow options, powered by SCIEX and supported by third-party collaborators across the proteomics ecosystem

Proteomics studies are only as strong as the full workflow, from separation and chromatography through acquisition and data processing. That’s why SCIEX works with third-party collaborators: to give researchers flexibility to build the right end-to-end workflow for their lab, while helping ensure the pieces work together for confident, reproducible results.

Proteomics FAQs

What is LC‑MS/MS proteomics, and why is LC–MS/MS the dominant technology?

Proteomics is the large-scale study of proteins, including their identification, quantitation, post-translational modifications (PTMs), and proteoforms across biological conditions. LC–MS/MS is the dominant technology because it combines high-resolution liquid chromatography with highly specific mass spectrometry and tandem MS detection. This enables deep coverage of complex samples while supporting both discovery and targeted quantitative workflows in a single analytical platform.

What is shotgun (bottom-up) proteomics?

Shotgun, or bottom-up, proteomics is a widely used approach where proteins are enzymatically digested into peptides prior to LC–MS/MS analysis. This strategy enables broad protein identification and quantitation across complex biological samples and supports the analysis of PTMs. Both data-dependent and data-independent acquisition methods are commonly used in shotgun proteomics workflows.

What is the difference between DDA (IDA) and DIA proteomics?

In data-dependent acquisition (DDA) or information-dependent acquisition (IDA), the mass spectrometer selects a subset of precursor ions for fragmentation in real time, which can maximize identifications but often leads to missing values across large sample sets. Data independent acquisition (DIA), including Zeno SWATH DIA and ZT Scan DIA, fragments all ions within defined m/z windows throughout the run. This creates a comprehensive and reproducible dataset that supports more consistent quantitation across cohorts, with data analysis playing a central role.

What problem does DIA or SWATH acquisition solve in proteomics?

DIA and SWATH acquisition address the issue of stochastic sampling and missing values commonly observed in DDA workflows. By systematically sampling the entire precursor space in every run, DIA enables more consistent peptide detection and quantitation across large sample sets, making it particularly well suited for translational, clinical, and systems biology studies.

What is targeted proteomics, and when should it be used?

Targeted proteomics focuses on a predefined list of peptides to achieve highly robust and reproducible quantitation. Multiple reaction monitoring (MRM) on triple quadrupole mass spectrometers is commonly used for verification, validation, and regulated studies. Targeted approaches are typically applied after discovery workflows to confirm and quantify proteins of interest across large numbers of samples.

Should I use a QTOF or a triple quadrupole for proteomics?

The choice depends on the measurement objective. QTOF systems are commonly used for discovery and broad profiling using DDA or DIA workflows, while triple quadrupole instruments are preferred for targeted quantitation using MRM when peptide targets are well defined. Many laboratories use both approaches, combining discovery-driven hypothesis generation with targeted verification and validation.

How do researchers balance depth, throughput, and robustness in proteomics?

Proteomics involves trade-offs between depth of coverage, sample throughput, and operational robustness. Nanoflow LC can maximize sensitivity and depth, while micro or analytical flow LC often improves robustness and reproducibility for high-throughput studies. Successful workflows typically prioritize stable, reproducible performance first, then optimize depth through method design, fractionation, or targeted follow-up rather than relying on a single parameter change.

How does SCIEX define proteomics performance beyond instrument sensitivity?

In practical proteomics, performance is determined by the entire analytical system, not just raw sensitivity. Chromatographic reproducibility, ionization stability, acquisition speed relative to chromatographic peak widths, and data processing strategy all contribute to meaningful results. SCIEX proteomics workflows are designed with this system-level perspective to support reproducible discovery and quantitative confidence across real-world studies.