Biomedical Big Data
Focus: protein quantification
The new protein can be a new protein, it may also be known structural protein of unknown function, but may also be aware of the new features of the protein structure.
The new protein can be identified using the following method.
Based on the genome, may genome coding region into the database the theoretical protein database using the translated amino acid codon, there are three versions accurately, can knock . 1 base, 2 bases, . 3 bases, etc. , taking into account the positive and negative factors chains, there are 3 * 2 = 6 possibilities. Based on the transcriptome translation, the use of search information database of known protein, high accuracy. denovo method, i.e., de novo sequencing method comprehensive comparison of reliability values based on scoring or p-value , etc.,
It can be integrated using the above method.
After getting raw data, as part of a low peak of many proteins is not easily MSMR perceived, while the analysis period is sub-sampled amount less quantitative more difficult, so this data filter. You can use pFind be open on a first-searching after a full investigation of precision, in order to reduce errors and search large libraries, in order to reduce the small error filter.
Protein identification probability calculation was based on data confidence is not directed research oriented, i.e., do not calculate the probability of the identification of the individual proteins, only the calculation made to the same batch of data, while the data can not merge different data processing directly. This is also the multi-batch quality control of content that need attention. Search engines use more than 2 engines optimum combination model is Mascot the X-+ .
It will be modified after protein translation. Modification of the status quo with regard to spectrum identification rate is low , that is not identified protein modification, these unrecognized modified so that expression of the protein to be underestimated. Modified into modified in vivo, in vitro and the modified amino acid mutations, the situation in vivo is a natural modification, post-translational modification, most of the modification is modified in vivo. Artificially modified in vitro modification, used in experimental research. Amino acid by amino acid mutations are expanded phosphorylated protein species.
Specifically, phospho 10 ^ 4 or 10 ^ 5 species ubiquitination scalable identified glycosylation complex, difficult to identify.
The principle is modified to identify the normal and modified two kinds of spectra comparison, the y- value increases, the proof modification is present. The difficulty lies in identifying modified variety, the abundance of low-modified less difficult to detect, often modified dynamic changes, such as the type of phosphorylation occurs or does not occur ^ loci. Modification of the contents of the study, the following four aspects, including modification of identification, modification quantitative modification network, a new modification of identification.
Routine modifications of the accreditation process for modification of an existing identified:
First, specify the type of modification, a modified type comprising a fixed and a variable modification modified, the modification is a fixed point by a 100% occurrence modified, is modified by a variable point occur necessarily modified. Through a database search to find the modified type of modification, the modified peptides and modification sites. When quality control, can be modified in vitro for directly peptides quality; For in vivo modifications, abundant proteins may be further modified with non-modified peptide separated from quality control, for the peptide to the low abundance proteins quality value card Quality . Site-after quality control peptide quality control, EG : phosphors software can be modified for the phosphorylation of identification.
Explore new modification can be used to identify non-restriction-modification:
While not specify the type of modification, the modified predetermined mass range, sequence by the presence of the modified information in the database match or map matching, to find and type of modification sites for modification, the final quality control.
Can use a combination of methods, fewer samples taken does not specify the type of modification is added, then the resulting modified type, added to the identified routine modifications to the process according to the type of modification obtained thereby specifying the types of modifications. Common software Mascot .
Although the multi-variable modifications makes search library sensitivity decreases, but first of all to ensure accuracy. Using multiple batches library search strategy, that is, each one modification as a search, there are n kinds of modifications are parallel n times search, instead of N kinds of modifications at the same time search.
Identification and modification of biological processes, to explain the biological process by modifying all substances measured metabolic pathway.