Editing Proteomics (section)

=== Protein detection with antibodies (immunoassays) ===
[[Antibodies]] to particular proteins, or their modified forms, have been used in [[biochemistry]] and [[cell biology]] studies. These are among the most common tools used by molecular biologists today. There are several specific techniques and protocols that use antibodies for protein detection. The [[enzyme-linked immunosorbent assay]] (ELISA) has been used for decades to detect and quantitatively measure proteins in samples.  The [[western blot]] may be used for detection and quantification of individual proteins, where in an initial step, a complex protein mixture is separated using [[SDS-PAGE]] and then the protein of interest is identified using an antibody.{{citation needed|date=April 2023}}

Modified proteins may be studied by developing an [[antibody]] specific to that modification. For example, some antibodies only recognize certain proteins when they are tyrosine-[[phosphorylated]], they are known as phospho-specific antibodies. Also, there are antibodies specific to other modifications. These may be used to determine the set of proteins that have undergone the modification of interest.{{citation needed|date=April 2023}}

Immunoassays can also be carried out using recombinantly generated immunoglobulin derivatives or synthetically designed protein scaffolds that are selected for high antigen specificity. Such binders include single domain antibody fragments (Nanobodies),<ref>{{cite journal | vauthors = Arbabi Ghahroudi M, Desmyter A, Wyns L, Hamers R, Muyldermans S | title = Selection and identification of single domain antibody fragments from camel heavy-chain antibodies | journal = FEBS Letters | volume = 414 | issue = 3 | pages = 521–526 | date = September 1997 | pmid = 9323027 | doi = 10.1016/S0014-5793(97)01062-4 | s2cid = 5988844 | doi-access = free | bibcode = 1997FEBSL.414..521A }}</ref> designed ankyrin repeat proteins (DARPins)<ref>{{cite journal | vauthors = Stumpp MT, Binz HK, Amstutz P | title = DARPins: a new generation of protein therapeutics | journal = Drug Discovery Today | volume = 13 | issue = 15–16 | pages = 695–701 | date = August 2008 | pmid = 18621567 | doi = 10.1016/j.drudis.2008.04.013 }}</ref> and aptamers.<ref>{{cite journal | vauthors = Jayasena SD | title = Aptamers: an emerging class of molecules that rival antibodies in diagnostics | journal = Clinical Chemistry | volume = 45 | issue = 9 | pages = 1628–1650 | date = September 1999 | pmid = 10471678 | doi = 10.1093/clinchem/45.9.1628 | doi-access = free }}</ref>

Disease detection at the molecular level is driving the emerging revolution of early diagnosis and treatment. A challenge facing the field is that protein biomarkers for early diagnosis may be present in very low abundance. The lower limit of detection with conventional immunoassay technology is the upper femtomolar range (10<sup>−13</sup> M). Digital immunoassay technology has improved detection sensitivity three logs, to the attomolar range (10<sup>−16</sup> M). This capability has the potential to open new advances in diagnostics and therapeutics, but such technologies have been relegated to manual procedures that are not well suited for efficient routine use.<ref>{{cite journal | vauthors = Wilson DH, Rissin DM, Kan CW, Fournier DR, Piech T, Campbell TG, Meyer RE, Fishburn MW, Cabrera C, Patel PP, Frew E, Chen Y, Chang L, Ferrell EP, von Einem V, McGuigan W, Reinhardt M, Sayer H, Vielsack C, Duffy DC | display-authors = 6 | title = The Simoa HD-1 Analyzer: A Novel Fully Automated Digital Immunoassay Analyzer with Single-Molecule Sensitivity and Multiplexing | journal = Journal of Laboratory Automation | volume = 21 | issue = 4 | pages = 533–547 | date = August 2016 | pmid = 26077162 | doi = 10.1177/2211068215589580 | doi-access = free }}</ref>