Learn about methods and technologies for peptide and protein analysis by high performance liquid chromatography and mass spectrometry (LC/MS). Understand sample prep tools, mass and isotope labeling strategies for quantitative proteomics, and the basics of MS data and analysis.

  • Proteomics
  • Cell lysis
  • Protein enrichment
  • Trypsin digestion
  • Peptide clean-up
  • C18
  • Sample prep 
  • Isobaric mass tagging
  • Stable isotope labeling
  • Metabolic labeling
  • Tandem mass spec
  • MS/MS
  • LC/MS
  • MALDI
  • Orbitrap
  • Technical handbooks
  • Protein methods articles
  • Product application notes
  • Support center resources
  • Protocols
  • Product selection guides

Protein mass spectrometry features

Methods article

A review of the history, applications and methodology of mass spectrometry, including ionization (ESA, MALDI), mass analyzers (TOF, quadrupole, ion trap), ion detectors, MS/MS, LC-MS/MS and sample prep.

Selection guide

Because the proteome is so complex, there is no one standard method for preparing protein samples for MS analysis. Protocols differ depending on the type of sample, experiment and method of analysis.


Protein mass spectrometry learning resources

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Type Title
Handbook Protein Research Handbook (2016)
Handbook Thermo Scientific Reagents for Quantitative Proteomics (2014)
Handbook Thermo Scientific Products for Mass Spectrometry Sample Preparation (2014)
Handbook Thermo Scientific Controls and Standards for Mass Spectrometry (2015)
Handbook Thermo Scientific Reagents for Mass Spectrometry (2015 New Product Guide)
Methods article The Pierce Protein Methods Library
Methods article An Overview of Mass Spectrometry (for Protein Analysis)
Methods article Quantitative Proteomics
Methods article Sample Preparation for Mass Spectrometry
Methods article An Overview of Post-Translational Modification
Methods article Phosphorylation
Methods article Glycosylation
Methods article Peptide Design
Methods article Peptide Synthesis
Methods article Amino Acid Physical Properties
Selection guide Workflow for Protein Mass Spectrometry (Selection Guide)
Selection guide Sample Prep for Mass Spectrometry (Selection Guide)
Selection guide Protein Quantitation Using Mass Spectrometry (Selection Guide)
Application note Product Application Notes
Application note Specific labeling, enrichment and quantitation of S-nitrosylated peptides using iodoTMT reagents. Measure protein and peptide cysteine modifications using multiplex quantitative mass spectrometry.
Application note A versatile mass spectrometry sample preparation procedure for complex protein samples. Prepare high-quality peptide digests with high recovery from cultured cells.
Application note Quantitative cancer stem cell phosphoprotein profiling. Using tandem mass labeling and LC-MS/MS to profile perturbations of an autocrine loop.
Application note Cell-free protein expression system for generating stable isotope-labeled proteins. Rapidly express protein standards for quantitative mass spectrometry.
Application note Calibration solutions for Thermo Scientific Mass Spectrometers. Ready-to-use standards enable quick instrument calibration.
Application note Develop mid- to high-throughput SRM and MRM assays. New application-specific peptide libraries for quantitative mass spectrometry workflows.
Application note Optimize liquid chromatography with a peptide retention time calibration mixture. New mixture of 15 heavy peptides streamlines assay design for targeted peptide quantification.
Application note Selective enrichment of sialylated glycopeptides using TiO2 beads. Affinity purification of glycoproteins for mass spectrometry based on titanium dioxide beads (TiO2).

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Browse protein biology learning center content by collection (resource type) — protein methods articles, product application notes, selection guides, webinars, technical handbooks, etc.

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