Protein analysis by shotgun/bottom-up proteomics
According to Genome Sequencing Project statistics (http://www. ncbi. nlm. nih.
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …
Less label, more free: approaches in label‐free quantitative mass spectrometry
In this review we examine techniques, software, and statistical analyses used in label‐free
quantitative proteomics studies for area under the curve and spectral counting approaches …
quantitative proteomics studies for area under the curve and spectral counting approaches …
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
AI Nesvizhskii - Journal of proteomics, 2010 - Elsevier
This manuscript provides a comprehensive review of the peptide and protein identification
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …
A face in the crowd: recognizing peptides through database search
Peptide identification via tandem mass spectrometry sequence database searching is a key
method in the array of tools available to the proteomics researcher. The ability to rapidly and …
method in the array of tools available to the proteomics researcher. The ability to rapidly and …
False discovery rates of protein identifications: a strike against the two-peptide rule
Most proteomics studies attempt to maximize the number of peptide identifications and
subsequently infer proteins containing two or more peptides as reliable protein …
subsequently infer proteins containing two or more peptides as reliable protein …
Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies
Database-searching programs generally identify only a fraction of the spectra acquired in a
standard LC/MS/MS study of digested proteins. Subtle variations in database-searching …
standard LC/MS/MS study of digested proteins. Subtle variations in database-searching …
Protein inference: a review
Assembling peptides identified from tandem mass spectra into a list of proteins, referred to
as protein inference, is a critical step in proteomics research. Due to the existence of …
as protein inference, is a critical step in proteomics research. Due to the existence of …
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
The problem of identifying proteins from a shotgun proteomics experiment has not been
definitively solved. Identifying the proteins in a sample requires ranking them, ideally with …
definitively solved. Identifying the proteins in a sample requires ranking them, ideally with …
Unrestricted identification of modified proteins using MS/MS
Proteins undergo PTM, which modulates their structure and regulates their function.
Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap …
Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap …
Machine learning applications in proteomics research: How the past can boost the future
Machine learning is a subdiscipline within artificial intelligence that focuses on algorithms
that allow computers to learn solving a (complex) problem from existing data. This ability can …
that allow computers to learn solving a (complex) problem from existing data. This ability can …