TABLE 1.
2-D gel separation | MALDI MS | LC-MS/MS | LC-MRM MS | Protein/antibody arrays | |
---|---|---|---|---|---|
Purpose | Profiling, separation and identification | Profiling | Inventory and identification | Targeted protein quantitation | Targeted protein detection |
Protein detection and identification | Protein pI and MW. Identification by peptide mapping and sequencing, | Detection of intact peptides and proteins | Identification via peptide sequences. | Peptide specific MS/MS transitions. | Detection using antibodies or ligands |
Quantitation | Semi-quantitative | Semiquantitative | Semiquantitative | Quantitative, labeled reference peptides. Label free techniques | Not quantitative |
PTM detection | Yes | No | Yes | Yes | Yes |
Throughput | Low | High | High | Low | High |
Reproducibility | High | High | High | High | High |
Sensitivity | Moderate | low | High | High | High |
Depth of analysis | 100–1,000 proteins | 100–300 peaks | 500–4,000 proteins | 1–100 proteins | 0–500 proteins |
Major disadvantages | pI and MW range limitations. Contamination by polysaccharides and nucleic acids | Detection of abundant proteins. Limited MW range (2–30 kDa). No identification. | High false discovery rate | Cost of labeled peptides for absolute quantitation | Antibody specificity and availability. Only known proteins can be detected. |
Definition of abbreviations: 2-D = two-dimensional; LC-MRM MS = liquid chromatography coupled to multiple reaction monitoring mass spectrometry; LC-MS/MS = liquid chromatography coupled to tandem mass spectrometry; MALDI MS = matrix-assisted laser desorption ionization mass spectrometry; ; MW = molecular weight; pI = isoelectric point; PTM = posttranslational modification.