Editing Proteomics (section)

==Bioinformatics for proteomics (proteome informatics)==
Much proteomics data is collected with the help of high throughput technologies such as [[mass spectrometry]] and microarray. It would often take weeks or months to analyze the data and perform comparisons by hand. For this reason, biologists and chemists are collaborating with computer scientists and mathematicians to create programs and pipeline to computationally analyze the protein data. Using [[bioinformatics]] techniques, researchers are capable of faster analysis and data storage. A good place to find lists of current programs and databases is on the [[ExPASy]] bioinformatics resource portal. The applications of bioinformatics-based proteomics include medicine, disease diagnosis, biomarker identification, and many more.

===Protein identification===
Mass spectrometry and microarray produce peptide fragmentation information but do not give identification of specific proteins present in the original sample. Due to the lack of specific protein identification, past researchers were forced to decipher the peptide fragments themselves. However, there are currently programs available for protein identification. These programs take the peptide sequences output from mass spectrometry and microarray and return information about matching or similar proteins. This is done through algorithms implemented by the program which perform alignments with proteins from known databases such as UniProt<ref>{{cite web|url=https://www.uniprot.org/|title=UniProt|website=www.uniprot.org}}</ref> and [[PROSITE]]<ref>{{cite web|url=http://prosite.expasy.org/|title=ExPASy - PROSITE|website=prosite.expasy.org}}</ref> to predict what proteins are in the sample with a degree of certainty.

===Protein structure===
{{main|Protein structure prediction}}
The [[biomolecular structure]] forms the 3D configuration of the protein. Understanding the protein's structure aids in the identification of the protein's interactions and function. It used to be that the 3D structure of proteins could only be determined using [[X-ray crystallography]] and [[NMR spectroscopy]]. As of 2017, [[Cryo-electron microscopy]] is a leading technique, solving difficulties with crystallization (in X-ray crystallography) and conformational ambiguity (in NMR); resolution was 2.2Å as of 2015. Now, through bioinformatics, there are computer programs that can in some cases predict and model the structure of proteins. These programs use the chemical properties of amino acids and structural properties of known proteins to predict the 3D model of sample proteins. This also allows scientists to model protein interactions on a larger scale. In addition, biomedical engineers are developing methods to factor in the flexibility of protein structures to make comparisons and predictions.<ref>{{cite journal | vauthors = Wang HW, Chu CH, Wang WC, Pai TW | title = A local average distance descriptor for flexible protein structure comparison | journal = BMC Bioinformatics | volume = 15 | issue = 95 | pages = 95 | date = April 2014 | pmid = 24694083 | pmc = 3992163 | doi = 10.1186/1471-2105-15-95 | doi-access = free }}</ref>

===Post-translational modifications===
Most programs available for protein analysis are not written for proteins that have undergone [[post-translational modifications]].<ref>{{cite journal | vauthors = Petrov D, Margreitter C, Grandits M, Oostenbrink C, Zagrovic B | title = A systematic framework for molecular dynamics simulations of protein post-translational modifications | journal = PLOS Computational Biology | volume = 9 | issue = 7 | pages = e1003154 | date = July 2013 | pmid = 23874192 | pmc = 3715417 | doi = 10.1371/journal.pcbi.1003154 | bibcode = 2013PLSCB...9E3154P | doi-access = free }}</ref> Some programs will accept post-translational modifications to aid in protein identification but then ignore the modification during further protein analysis. It is important to account for these modifications since they can affect the protein's structure. In turn, computational analysis of post-translational modifications has gained the attention of the scientific community. The current post-translational modification programs are only predictive.<ref>{{cite journal | vauthors = Margreitter C, Petrov D, Zagrovic B | title = Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications | journal = Nucleic Acids Research | volume = 41 | issue = Web Server issue | pages = W422–W426 | date = July 2013 | pmid = 23703210 | pmc = 3692090 | doi = 10.1093/nar/gkt416 }}</ref> Chemists, biologists and computer scientists are working together to create and introduce new pipelines that allow for analysis of post-translational modifications that have been experimentally identified for their effect on the protein's structure and function.

===Computational methods in studying protein biomarkers===
One example of the use of bioinformatics and the use of computational methods is the study of protein biomarkers. Computational predictive models<ref>{{cite journal | vauthors = Maron JL, Alterovitz G, Ramoni M, Johnson KL, Bianchi DW | title = High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women | journal = Proteomics. Clinical Applications | volume = 3 | issue = 12 | pages = 1389–1396 | date = December 2009 | pmid = 20186258 | pmc = 2825712 | doi = 10.1002/prca.200900109 }}</ref> have shown that extensive and diverse feto-maternal protein trafficking occurs during pregnancy and can be readily detected non-invasively in maternal whole blood. This computational approach circumvented a major limitation, the abundance of maternal proteins interfering with the detection of [[fetal protein]]s, to fetal proteomic analysis of maternal blood. Computational models can use fetal gene transcripts previously identified in maternal [[whole blood]] to create a comprehensive proteomic network of the term [[neonate]]. Such work shows that the fetal proteins detected in pregnant woman's blood originate from a diverse group of tissues and organs from the developing fetus. The proteomic networks contain many [[biomarker (medicine)|biomarkers]] that are proxies for development and illustrate the potential clinical application of this technology as a way to monitor normal and abnormal fetal development.

An information-theoretic framework has also been introduced for [[biomarker (medicine)|biomarker]] discovery, integrating biofluid and tissue information.<ref name="Alterovitz_2008">{{cite book | vauthors = Alterovitz G, Xiang M, Liu J, Chang A, Ramoni MF |title=Biocomputing 2008 |chapter=System-wide peripheral biomarker discovery using information theory |journal=Pacific Symposium on Biocomputing |pages=231–42 |year=2008 |pmid=18229689 |chapter-url=http://psb.stanford.edu/psb-online/proceedings/psb08/abstracts/2008_p231.html |doi=10.1142/9789812776136_0024 |isbn=9789812776082 }}</ref> This new approach takes advantage of functional synergy between certain biofluids and tissues with the potential for clinically significant findings not possible if tissues and biofluids were considered individually. By conceptualizing tissue-biofluid as information channels, significant biofluid proxies can be identified and then used for the guided development of clinical diagnostics. Candidate biomarkers are then predicted based on information transfer criteria across the tissue-biofluid channels. Significant biofluid-tissue relationships can be used to prioritize clinical validation of biomarkers.<ref name="Alterovitz_2008" />