Table 1.
Proteomics toolbox.
| Proteomics Toolbox | Technical Process | Strengths | Limitations | Reference | ||
|---|---|---|---|---|---|---|
| Targeted Approaches | MRM, SRM | (1) Primary mass spectrometry scans to screen out parent ions that are consistent with the specificity of the target molecule. (2) Collision and fragmentation of parent ions to remove interfering ions. (3) Mass spectrometry signals collected from selected specific ions | (1) High sensitivity (2) Good accuracy (3) Good reproducibility (4) High-throughput |
(1) Only preselected proteins can be detected (2) No screening analysis |
[33,34] | |
| PRM | (1) Select targeted peptides. (2) Define acquisition method. (3) Preliminary experiment to adjust the parameters and target peptide fragment. (4) Perform PRM analysis. (5) Analyze data | (1) Simpler and cheaper. (2) Wider linear detection range. (3) Higher selectivity, better sensitivity and better reproducibility | (1) Only preselected proteins can be detected (2) No screening analysis (3) When the number of peptides to be analyzed is large it is necessary to fine-tune the MS collection parameters |
[35,36] | ||
| Untargeted Approaches | DDA | iTRAQ/TMT | (1) Enzymatic or chemical fragmentation. (2) Differential labeling using iTRAQ/TMT reagent. (3) Mixed labeled protein samples analyzed by tandem mass spectrometry. (4) Data analysis | (1) Good repeatability. (2) Mature method. (3) Wide range of sample sources | (1) Easily contaminated by other proteins in the sample (2) Maximum 12 channels at a time |
[37] |
| Label-free | (1) Protein extraction. (2) Protein digestion. (3) LC–MS/MS analysis. (4) Data analysis | (1) Low cost (2) Not limited by the number of samples. (3) Wide range of application |
(1) Highly dependent on machine stability. (2) Quantitative results can be unreliable | [38] | ||
| DIA | SWATH | (1) Sample digestion (2) Consecutive, adjacent precursor ion windows (SWATHs) scanned using a Triple TOF MS (3) Data analyzed using bioinformatics and a relevant reference spectral library |
(1) Good reproducibility. (2) Less affected by high-abundance proteins | Quality of spectral library for data analysis | [32,39,40,41] | |