Mass spectrometryMass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio.
Tandem mass spectrometryTandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides. The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q).
Protein sequencingProtein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information (one or more sequence tags) to identify it with reference to databases of protein sequences derived from the conceptual translation of genes. The two major direct methods of protein sequencing are mass spectrometry and Edman degradation using a protein sequenator (sequencer).
Ion-mobility spectrometry–mass spectrometryIon mobility spectrometry–mass spectrometry (IMS-MS) is an analytical chemistry method that separates gas phase ions based on their interaction with a collision gas and their masses. In the first step, the ions are separated according to their mobility through a buffer gas on a millisecond timescale using an ion mobility spectrometer. The separated ions are then introduced into a mass analyzer in a second step where their mass-to-charge ratios can be determined on a microsecond timescale.
ProteomicsProteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system.
False discovery rateIn statistics, the false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the expected proportion of "discoveries" (rejected null hypotheses) that are false (incorrect rejections of the null). Equivalently, the FDR is the expected ratio of the number of false positive classifications (false discoveries) to the total number of positive classifications (rejections of the null).
False positive rateIn statistics, when performing multiple comparisons, a false positive ratio (also known as fall-out or false alarm ratio) is the probability of falsely rejecting the null hypothesis for a particular test. The false positive rate is calculated as the ratio between the number of negative events wrongly categorized as positive (false positives) and the total number of actual negative events (regardless of classification). The false positive rate (or "false alarm rate") usually refers to the expectancy of the false positive ratio.
Cross-validation (statistics)Cross-validation, sometimes called rotation estimation or out-of-sample testing, is any of various similar model validation techniques for assessing how the results of a statistical analysis will generalize to an independent data set. Cross-validation is a resampling method that uses different portions of the data to test and train a model on different iterations. It is mainly used in settings where the goal is prediction, and one wants to estimate how accurately a predictive model will perform in practice.
ProteinProteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Statistical model validationIn statistics, model validation is the task of evaluating whether a chosen statistical model is appropriate or not. Oftentimes in statistical inference, inferences from models that appear to fit their data may be flukes, resulting in a misunderstanding by researchers of the actual relevance of their model. To combat this, model validation is used to test whether a statistical model can hold up to permutations in the data.
Regression validationIn statistics, regression validation is the process of deciding whether the numerical results quantifying hypothesized relationships between variables, obtained from regression analysis, are acceptable as descriptions of the data. The validation process can involve analyzing the goodness of fit of the regression, analyzing whether the regression residuals are random, and checking whether the model's predictive performance deteriorates substantially when applied to data that were not used in model estimation.
Family-wise error rateIn statistics, family-wise error rate (FWER) is the probability of making one or more false discoveries, or type I errors when performing multiple hypotheses tests. John Tukey developed in 1953 the concept of a familywise error rate as the probability of making a Type I error among a specified group, or "family," of tests. Ryan (1959) proposed the related concept of an experimentwise error rate, which is the probability of making a Type I error in a given experiment.
False positives and false negativesA false positive is an error in binary classification in which a test result incorrectly indicates the presence of a condition (such as a disease when the disease is not present), while a false negative is the opposite error, where the test result incorrectly indicates the absence of a condition when it is actually present. These are the two kinds of errors in a binary test, in contrast to the two kinds of correct result (a and a ).
Biological databaseBiological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.
Human taxonomyHuman taxonomy is the classification of the human species (systematic name Homo sapiens, Latin: "wise man") within zoological taxonomy. The systematic genus, Homo, is designed to include both anatomically modern humans and extinct varieties of archaic humans. Current humans have been designated as subspecies Homo sapiens sapiens, differentiated, according to some, from the direct ancestor, Homo sapiens idaltu (with some other research instead classifying idaltu and current humans as belonging to the same subspecies).
SequenceIn mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called elements, or terms). The number of elements (possibly infinite) is called the length of the sequence. Unlike a set, the same elements can appear multiple times at different positions in a sequence, and unlike a set, the order does matter. Formally, a sequence can be defined as a function from natural numbers (the positions of elements in the sequence) to the elements at each position.
HomoHomo () is the genus that emerged from the genus Australopithecus and encompasses the extant species Homo sapiens (modern humans) and several extinct species classified as either ancestral to or closely related to modern humans, including Homo erectus and Homo neanderthalensis. The oldest member of the genus is Homo habilis, with records of just over 2 million years ago. Homo, together with the genus Paranthropus, is probably sister to Australopithecus africanus, which itself had split from the lineage of Pan, the chimpanzees.
Homo rhodesiensisHomo rhodesiensis is the species name proposed by Arthur Smith Woodward (1921) to classify Kabwe 1 (the "Kabwe skull" or "Broken Hill skull", also "Rhodesian Man"), a Middle Stone Age fossil recovered from Broken Hill mine in Kabwe, Northern Rhodesia (now Zambia). In 2020, the skull was dated to 324,000 to 274,000 years ago. Other similar older specimens also exist. H. rhodesiensis is now widely considered a synonym of H. heidelbergensis. Other designations such as Homo sapiens arcaicus and Homo sapiens rhodesiensis have also been proposed.
Homo heidelbergensisHomo heidelbergensis (also H. erectus heidelbergensis, H. sapiens heidelbergensis) is an extinct species or subspecies of archaic human which existed during the Middle Pleistocene. It was subsumed as a subspecies of H. erectus in 1950 as H. e. heidelbergensis, but towards the end of the century, it was more widely classified as its own species. It is debated whether or not to constrain H.
Early modern humanEarly modern human (EMH) or anatomically modern human (AMH) are terms used to distinguish Homo sapiens (the only extant Hominina species) that are anatomically consistent with the range of phenotypes seen in contemporary humans, from extinct archaic human species. This distinction is useful especially for times and regions where anatomically modern and archaic humans co-existed, for example, in Paleolithic Europe.
