The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment

H Rodriguez, JC Zenklusen, LM Staudt, JH Doroshow… - Cell, 2021 - cell.com
When it comes to precision oncology, proteogenomics may provide better prospects to the
clinical characterization of tumors, help make a more accurate diagnosis of cancer, and …

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 …

Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950–Metabolites in Frozen Human Plasma [S]

JA Bowden, A Heckert, CZ Ulmer, CM Jones… - Journal of lipid …, 2017 - ASBMB
As the lipidomics field continues to advance, self-evaluation within the community is critical.
Here, we performed an interlaboratory comparison exercise for lipidomics using Standard …

A repository of assays to quantify 10,000 human proteins by SWATH-MS

G Rosenberger, CC Koh, T Guo, HL Röst, P Kouvonen… - Scientific data, 2014 - nature.com
Mass spectrometry is the method of choice for deep and reliable exploration of the (human)
proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets …

Options and considerations when selecting a quantitative proteomics strategy

B Domon, R Aebersold - Nature biotechnology, 2010 - nature.com
The vast majority of proteomic studies to date have relied on mass spectrometric techniques
to identify, and in some cases quantify, peptides that have been generated by proteolysis …

Repeatability and reproducibility in proteomic identifications by liquid chromatography− tandem mass spectrometry

DL Tabb, L Vega-Montoto, PA Rudnick… - Journal of proteome …, 2010 - ACS Publications
The complexity of proteomic instrumentation for LC-MS/MS introduces many possible
sources of variability. Data-dependent sampling of peptides constitutes a stochastic element …

Targeted quantitation of proteins by mass spectrometry

DC Liebler, LJ Zimmerman - Biochemistry, 2013 - ACS Publications
Quantitative measurement of proteins is one of the most fundamental analytical tasks in a
biochemistry laboratory, but widely used immunochemical methods often have limited …

Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets

A Chawade, E Alexandersson… - Journal of proteome …, 2014 - ACS Publications
High-throughput omics data often contain systematic biases introduced during various steps
of sample processing and data generation. As the source of these biases is usually …

[HTML][HTML] Mass spectrometry based biomarker discovery, verification, and validation–quality assurance and control of protein biomarker assays

CE Parker, CH Borchers - Molecular oncology, 2014 - Elsevier
In its early years, mass spectrometry (MS)-based proteomics focused on the cataloging of
proteins found in different species or different tissues. By 2005, proteomics was being used …

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

DJ Geiszler, AT Kong, DM Avtonomov, F Yu… - Molecular & Cellular …, 2021 - ASBMB
Open searching has proven to be an effective strategy for identifying both known and
unknown modifications in shotgun proteomics experiments. Rather than being limited to a …