They used two-dimensional gel electrophoresis and mass spectrometry to identify 82 proteins secreted by B. subtilis, only 48 of which had been predicted using the genome-based method of their previous paper.
Bovine serum from cell culture media and cellular debris can contaminate the collection of secreted proteins used for analysis.
[1] In addition, incubation time and conditions must be optimized so that the metabolic stress that can be induced by the lack of nutrients in SFM does not affect secretomic analysis.
More and more studies, especially those looking at the cancer secretome, are using in vivo methods to confirm the relevance of the results obtained in vitro.
[1] As an example, the SILAC method has been used successfully to distinguish between proteins secreted by human chondrocytes in culture and serum contaminants.
[14] An antibody microarray is a highly sensitive and high-throughput method for protein detection that has recently become part of secretomic analysis.
Antibodies, or another type of binder molecule, are fixed onto a solid support and a fluorescently labeled protein mixture is added.
Antibody microarrays are currently being used mostly to analyze human plasma samples but can also be used for cultured cells and body fluid secretomics, presenting a simple way to look for the presence of many proteins at one time.
[11] Besides being important in normal physiological processes, secreted proteins also have an integral role in tumorigenesis through cell growth, migration, invasion, and angiogenesis, making secretomics an excellent method for the discovery of cancer biomarkers.
Secretomic analysis of cancer cell lines or diseased tissue presents a simpler and more specific alternative for biomarker discovery.
Using secretomic analysis of prostate cell lines, one study was able to discover multiple proteins found in higher levels in the serum of cancer patients than in healthy controls.
[2] Secretomic analysis of breast cancer cell lines led to the discovery of the protein ALCAM as a new biomarker with promising diagnostic potential.
This type of analysis could help replace preimplantation genetic screening (PGS), which involves biopsy of embryonic cells and can be harmful to development.