Table 2.
Typical Proteomic approaches according to the investigation of how protein regulation in macroalgae can be influenced by abiotic stress.
| Macroalgae | Proteomic Approaches | Generating Raw Data | Alignment and Identification | Data Analysis | Reference |
|---|---|---|---|---|---|
| Gracilaria lemaneiformis (red algae) | Proteins analyzed by MS by a bottom–up approach (smaller peptides derived from enzymatic digestion of proteins) | 2D-Electrophoresis; MALDI-TOF MS | Mascot aligner; MoverZ and NCBI non-redundant protein database | Protein identification was accepted with a MASCOT score higher than 60 with more than five matched peptides. The MASCOT protein search was performed via all plants’ database. | [70] |
| Pyropia haitanensis (red algae) | Proteins analyzed by MS by a bottom–up approach | 2D-Electrophoresis; MALDI-TOF/TOF MS | Mascot aligner; NCBI and SwissProt database | According to the search engine parameters, scores greater than 65 (p < 0.05) were considered positive. | [25] |
| Pyropia orbicularis (red algae) | Proteins analyzed by MS by a bottom–up approach | 2D-Electrophoresis; Nano-LC-MS/MS coupled on-line to a LTQ Orbitrap Discovery system mass spectrometer | PEAKS Studio software. This database included P. orbicularis ESTs, Chondrus crispus genes, and Ectocarpus siliculosus genes, BLAST-P in NCBI database |
ExPASy Compute pI/MW tool; Protein functional classification using KEGG pathway analysis. The threshold was set to a minimal Significance of 1 × 10−3 and an identity percentage of greater than 25%. |
[23] |
| Sargassum fusiforme (brown algae) | Proteins analyzed by MS by a bottom–up approach | 2D-Electrophoresis; MALDI-TOF/TOF MS | Mascot aligner; NCBI non-redundant FASTA database and UniProt database | Protein functional classification using KEGG pathway analysis; Protein-protein association information evaluated with the STRING database against Phaeodactylum tricornutum database. Individual ion scores of more than 28 indicate identity or extensive homology (p < 0.05). | [71] |