New tools for improved proteomics results

Importance of the topic

Proteomic mass spectrometry plays a critical role in biology and clinical research by enabling comprehensive profiling of proteins, their abundance, modifications, and interactions. Standardized reagents and workflows enhance reproducibility, reduce hands-on time, and facilitate consistent results across laboratories.

• Streamlines complex sample preparation steps
• Enables accurate quantitation of proteins and post-translational modifications
• Supports rigorous instrument performance monitoring and calibration

Objectives and overview

This whitepaper introduces a complete portfolio of solutions for proteomic workflows, covering sample preparation (EasyPep kits), phosphopeptide enrichment (High-Select Fe-NTA Magnetic reagents), targeted protein quantitation (SureQuant kits and standards), isobaric labeling (TMTpro 18plex and Super Heavy TMTpro), protein crosslinking reagents (DSSO, DSBU, DSPP, TBDSPP, 6C-CysPAT), and LC-MS/MS system suitability and calibration standards.

Methodology and instrumentation

Reagents and protocols have been optimized for compatibility with diverse sample types—cell lines, tissues, plasma—and downstream applications including label-free quantitation, isobaric labeling, phosphopeptide enrichment, and targeted MS (SRM/PRM). Standardized workflows reduce sample prep from over 24 hours to under 4 hours. Quality control standards enable assessment of chromatography and mass spectrometer performance over a wide mass range.

Main results and discussion

EasyPep kits delivered equivalent or higher peptide and protein identifications compared to traditional workflows with more than 90% digestion efficiency in under 4 hours. High-Select Fe-NTA enrichment achieved over 90% phosphopeptide selectivity in under 45 minutes. SureQuant modules provided precise multiplexed quantitation of key signaling proteins and phosphoproteins in tissue and cell lysates. TMTpro 18plex reagents expanded multiplexing capacity with accurate reporter-ion quantitation across serially diluted yeast standards. Super Heavy TMTpro enabled 2D multiplexed targeted workflows with reduced interference. MS-cleavable crosslinkers DSSO and DSBU, and enrichable reagents DSPP and TBDSPP, enhanced identification of protein–protein crosslinks. The 6C-CysPAT reagent allowed selective enrichment of cysteine peptides for stress-induced proteome changes. Calibration standards—7×5 peptide mix, yeast and HeLa digests with PRTC, small molecule mixes, and FlexMix solution—provided robust QC for LC and MS systems.

Benefits and practical applications

These integrated reagents and standards support high-throughput proteomics, targeted pathway analysis, PTM mapping, structural proteomics, and routine instrument QC. Labs benefit from time savings, reduced protocol variability, increased multiplexing, and reliable instrument calibration.

Future trends and potential uses

Advances will focus on deeper proteome coverage, higher multiplexing, streamlined crosslinking analysis, real-time QC automation, and integration with AI-driven data analysis. Emerging applications include single-cell proteomics, in vivo crosslinking, and expanded targeted diagnostics panels.

Conclusion

The Thermo Scientific portfolio offers end-to-end solutions that dramatically simplify proteomic workflows, improve data quality, and ensure reproducible results. Adoption of these standardized reagents and protocols accelerates discovery and strengthens confidence in proteomics data.

Used instrumentation

• Thermo Scientific UltiMate 3000 RSLCnano System
• Dionex UltiMate 3000 RSLCnano System
• Thermo Scientific Q Exactive HF and HF-X Orbitrap Mass Spectrometers
• Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer
• Thermo Scientific TSQ Quantis Triple Quadrupole Mass Spectrometer
• Thermo Scientific Orbitrap IQ-X Tribrid Mass Spectrometer
• Thermo Scientific EASY-nLC 1000 and Velos Pro MS
• Thermo Scientific KingFisher magnetic particle processors