Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

DP Donnelly, CM Rawlins, CJ DeHart, L Fornelli… - Nature …, 2019 - nature.com
One gene can give rise to many functionally distinct proteoforms, each of which has a
characteristic molecular mass. Top-down mass spectrometry enables the analysis of intact …

A high-stringency blueprint of the human proteome

S Adhikari, EC Nice, EW Deutsch, L Lane… - Nature …, 2020 - nature.com
Abstract The Human Proteome Organization (HUPO) launched the Human Proteome Project
(HPP) in 2010, creating an international framework for global collaboration, data sharing …

The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells

RD Melani, VR Gerbasi, LC Anderson, JW Sikora… - Science, 2022 - science.org
Human biology is tightly linked to proteins, yet most measurements do not precisely
determine alternatively spliced sequences or posttranslational modifications. Here, we …

Protein analysis by shotgun/bottom-up proteomics

Y Zhang, BR Fonslow, B Shan, MC Baek… - Chemical …, 2013 - ACS Publications
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 …

[HTML][HTML] Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics

AC Peterson, JD Russell, DJ Bailey… - Molecular & cellular …, 2012 - Elsevier
Selected reaction monitoring on a triple quadrupole mass spectrometer is currently
experiencing a renaissance within the proteomics community for its, as yet, unparalleled …

Andromeda: a peptide search engine integrated into the MaxQuant environment

J Cox, N Neuhauser, A Michalski… - Journal of proteome …, 2011 - ACS Publications
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in
sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel …

The integrin adhesome: from genes and proteins to human disease

SE Winograd-Katz, R Fässler, B Geiger… - … reviews Molecular cell …, 2014 - nature.com
The adhesive interactions of cells with their environment through the integrin family of
transmembrane receptors have key roles in regulating multiple aspects of cellular …

[HTML][HTML] Status of large-scale analysis of post-translational modifications by mass spectrometry

JV Olsen, M Mann - Molecular & cellular proteomics, 2013 - Elsevier
Cellular function can be controlled through the gene expression program, but often protein
post-translational modifications (PTMs) provide a more precise and elegant mechanism. Key …

MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra

V Dorfer, P Pichler, T Stranzl, J Stadlmann… - Journal of proteome …, 2014 - ACS Publications
Today's highly accurate spectra provided by modern tandem mass spectrometers offer
considerable advantages for the analysis of proteomic samples of increased complexity …

Deep proteome and transcriptome map** of a human cancer cell line

N Nagaraj, JR Wisniewski, T Geiger, J Cox… - Molecular systems …, 2011 - embopress.org
While the number and identity of proteins expressed in a single human cell type is currently
unknown, this fundamental question can be addressed by advanced mass spectrometry …