Method of identification of entities from mass spectra

2:

• The method according to claim 1, wherein in the step c), the calculation involves calculating maximal probability of candidate identity or calculating probability of candidate identity, optionally using Bayes' Theorem.

3:

• The method according to claim 1, wherein in the step b) the value of prevalence is calculated based on at least one of population frequency of said entity, probability of modification of said entity in the environment, probability of modification of said entity during the analysis step.

4:

• The method according to claim 1, wherein in the steps b) and c), the value of prevalence is expressed as prior probability or as prior-like probability.

5:

• The method according to claim 1, wherein the entity is selected from a peptide, a protein, a lipid, a nucleic acid, a metabolite and a molecule having the molecular weight of up to 2000 mol/g.

8:

• The method according to claim 1, wherein the entities are proteins, wherein the step of obtaining the candidate identities of an entity in step b) includes database search in database of peptide variants, and wherein the method is used for identification of mutant and polymorphic proteins from mass spectra of proteome, with alterations already observed globally on nucleotide level

9:

• The method according to claim 1, wherein the entities are peptides, further comprising the steps of:
• e) matching of entities determined as polymorphic or germline peptides to database of origins,
• and wherein the method is used for authentication of cell lines or identification of a person from mass spectra of proteome.

10:

• The method according to claim 1, wherein the entities are non-host peptides, wherein in the step b) the prevalence is expressed as prior or prior-like probability and prevalence of non-host peptides is scaled down according to prevalence of non-host organism,
• and wherein the method is used for identification of non-host organism of known prevalence from mass spectra of proteome of host organism, for instance to identify microbial infection or colonization of the host.

11:

• The method according to claim 6, wherein the entities are non-host peptides, wherein in the step b) in obtaining the candidate identities, peptides uniquely mapping to non-host organism are added to enumerated peptides of host organism and prevalence of non-host peptides is lower than of any host peptide,
• and wherein the method is used for identification of non-host organism of unknown prevalence from mass spectra of proteome of host organism.

12:

• The method according to claim 1, wherein the entities are donor peptides, wherein in the step b) the prevalence of donor peptides is scaled according to their prevalence among recipient peptides,
• and wherein the method is used for identification of proteins originating from grafted tissue in recipient.

13:

• The method according to claim 1, wherein the entities are peptides, the method further comprising the step of:
• e) selecting somatic mutant peptides attributable to tumour,
• wherein the method is used for identification of presence of a tumour from mass spectra of circulating proteins or estimation of tumour biological characteristics through increase in number of somatic mutations.

14:

• The method according to claim 1, wherein the entities are peptides, the method further comprising the step of:
• e) selection and quantification of polymorphic peptides attributable to donor,
• wherein the method is used for monitoring tissue or organ grafting and early detection of transplant rejection from mass spectra of biological material of recipient.

15:

• The method according to claim 1, wherein the entities are peptides, said method further comprising the steps of:
• e) calculating significance of match between two individuals based on polymorphic peptides,
• wherein the method is used for determination of presence of genetic relationship between two or more individuals from measured mass spectra of proteome.