The abc's (and xyz's) of peptide sequencing

By Hanno Steen, Matthias Mann. Nature reviews. Molecular cell biology, 2004

1,211 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/61313b8af26e91b863c6129387fc92e0df4f9949

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Citations in the corpus

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, background): “Peptides, as they elude from the reverse phase column at a particular time (retention time) are ionized, transferred into the gas phase, and selected ions are subjected to tandem mass spectrometry (MS/MS) sequencing to produce fragment ion spectra (MS/MS spectra) [16].”
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification (2008, methodology): “MS spectra contain peptide mass and intensity information, and the identity of the peptides is deduced by matching the MS/MS spectra against a sequence databas”
Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel (2019, background): “The major result of this is that the spectrum of fragmentation masses has the potential to identify a given peptide sequence, and in turn provide evidence of a protein being present in a given sample (Aebersold and Mann, 2016; Nesvizhskii, 2010; Steen and Mann, 2004; Zhang et al., 2012).”
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins (2006, background): “See Steen and Mann [65] for an introduction to peptide sequencing and confidence of peptide identification.”
De novo peptide sequencing by deep learning (2017, background): “Another challenge is that peptide fragmentation generates multiple types of ions, including a, b, c, x, y, z, internal cleavage, and immonium ions (38).”
The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes (2010, background): “The charge of an ion can be determined from resolved isotope peaks and the mass then be calculated (for more details on peptide fragmentation in a mass spectrometer consult the introductory review written by Steen and Mann (2004)).”
Decoding signalling networks by mass spectrometry-based proteomics (2010, background): “Most commonly they are collided with a low pressure of an inert gas (collision-induced dissociation (CID); see Ref”
Mass spectrometry–based proteomics turns quantitative (2005, background): “Indeed, it is not unusual for a weak peptide signal to give a clear sequence ladder leading to a high identification scor”
Correlation of mRNA and protein in complex biological samples (2009, positive): “Raising the required identiﬁcation scores reduces the number of false positive identiﬁcations, while at the same time increasing the false negative rate [79].”