NDLI: Rapid and deep human proteome analysis by single-dimension shotgun proteomics.

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Investigations on aberrant glycosylation of glycosphingolipids in colorectal cancer tissues using liquid chromatography and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS).

Rapid and deep human proteome analysis by single-dimension shotgun proteomics.

Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits.

Molecular responses of mouse macrophages to copper and copper oxide nanoparticles inferred from proteomic analyses.

Multi-dimensional co-separation analysis reveals protein-protein interactions defining plasma lipoprotein subspecies.

Quantitative phosphoproteomic study of pressure-overloaded mouse heart reveals dynamin-related protein 1 as a modulator of cardiac hypertrophy.

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics.

Interrogating cAMP-dependent kinase signaling in Jurkat T cells via a protein kinase A targeted immune-precipitation phosphoproteomics approach.

Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation.

Cell cycle regulation of microtubule interactomes: multi-layered regulation is critical for the interphase/mitosis transition.

High-throughput analysis of in vivo protein stability.

A label-free selected reaction monitoring workflow identifies a subset of pregnancy specific glycoproteins as potential predictive markers of early-onset pre-eclampsia.

Plasma membrane proteomics of tumor spheres identify CD166 as a novel marker for cancer stem-like cells in head and neck squamous cell carcinoma.

Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.

Exploring the N-glycosylation pathway in Chlamydomonas reinhardtii unravels novel complex structures.

Interactions affected by arginine methylation in the yeast protein-protein interaction network.

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data.

Interactome analysis reveals that C1QBP (complement component 1, q subcomponent binding protein) is associated with cancer cell chemotaxis and metastasis.

Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay.

Linking spermatid ribonucleic acid (RNA) binding protein and retrogene diversity to reproductive success.

A proteomic perspective of inbuilt viral protein regulation: pUL46 tegument protein is targeted for degradation by ICP0 during herpes simplex virus type 1 infection.

Regulation of stress-inducible phosphoprotein 1 nuclear retention by protein inhibitor of activated STAT PIAS1.

Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense.

Selective targeting of the cysteine proteome by thioredoxin and glutathione redox systems.

Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection.

Host-centric proteomics of stool: a novel strategy focused on intestinal responses to the gut microbiota.

A Specific PTPRC/CD45 Phosphorylation Event Governed by Stem Cell Chemokine CXCL12 Regulates Primitive Hematopoietic Cell Motility

Year: 2013 Volume: 12 Issue: 10

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Rapid and deep human proteome analysis by single-dimension shotgun proteomics.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Pirmoradian, Mohammad Budamgunta, Harshavardhan Chingin, Konstantin Zhang, Bo Astorga-Wells, Juan Zubarev, Roman A.
Description	Author Affiliation: Pirmoradian M ( Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-17177 Stockholm, Sweden)
Abstract	Multiparameter optimization of an LC-MS/MS shotgun proteomics experiment was performed without any hardware or software modification of the commercial instrument. Under the optimized experimental conditions, with a 50-cm-long separation column and a 4-h LC-MS run (including a 3-h optimized gradient), 4,825 protein groups and 37,550 peptides were identified in a single run and 5,354 protein groups and 56,390 peptides in a triplicate analysis of the A375 human cell line, for approximately 50% coverage of the expressed proteome. The major steps enabling such performance included optimization of the cell lysis and protein extraction, digestion of even insoluble cell debris, tailoring the LC gradient profile, and choosing the optimal dynamic exclusion window in data-dependent MS/MS, as well as the optimal m/z scan window.
File Format	HTM / HTML
ISSN	15359476
e-ISSN	15359484
DOI	10.1074/mcp.O113.028787
Journal	Molecular & Cellular Proteomics
Issue Number	11
Volume Number	12
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2013-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Proteomics Proteome Proteomics Cell Line Chromatography, Liquid Isolation & Purification Instrumentation Statistics & Numerical Data Tandem Mass Spectrometry Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Medicine Analytical Chemistry Molecular Biology Biochemistry

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Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.

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Rapid and deep human proteome analysis by single-dimension shotgun proteomics.

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