Proteomics and systems biology: current and future applications in the nutritional sciences (Q26829598)

M. E. Weeks

series ordinal

2

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language of work or name

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July 2011

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published in

Advances in Nutrition

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volume

2

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issue

4

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page(s)

355-64

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Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome

cites work

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The implications of human metabolic network topology for disease comorbidity

7 April 2017

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The human disease network

7 April 2017

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Global reconstruction of the human metabolic network based on genomic and bibliomic data

7 April 2017

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Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

7 April 2017

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Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

7 April 2017

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Correlation between protein and mRNA abundance in yeast

7 April 2017

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SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

7 April 2017

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Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome

7 April 2017

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Proteomics by mass spectrometry: approaches, advances, and applications

7 April 2017

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Multidimensional separations-based shotgun proteomics

7 April 2017

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Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer

7 April 2017

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Mass spectrometry-based proteomics turns quantitative

7 April 2017

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Urinary collagen fragments are significantly altered in diabetes: a link to pathophysiology

7 April 2017

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Identification of potential pathway mediation targets in Toll-like receptor signaling

7 April 2017

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The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks

7 April 2017

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mzML--a community standard for mass spectrometry data

7 April 2017

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Proteomics-based identification of differentially-expressed proteins including galectin-1 in the blood plasma of type 2 diabetic patients

7 April 2017

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Applications of genome-scale metabolic reconstructions

7 April 2017

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Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

7 April 2017

1 reference

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A model for random sampling and estimation of relative protein abundance in shotgun proteomics

7 April 2017

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Systems biology: a brief overview

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Computational systems biology

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Discussion on common data analysis strategies used in MS-based proteomics.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Patterns of human gene expression variance show strong associations with signaling network hierarchy

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Top-down protein characterization facilitated by ion/ion reactions on a quadrupole/time of flight platform.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Separation of peptide isomers with variant modified sites by high-resolution differential ion mobility spectrometry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Proteomics in nutrition: status quo and outlook for biomarkers and bioactives.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Altered retinoic acid metabolism in diabetic mouse kidney identified by O isotopic labeling and 2D mass spectrometry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

The SILAC fly allows for accurate protein quantification in vivo.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Towards genome-scale signalling network reconstructions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

DJ-1 and alpha-synuclein in human cerebrospinal fluid as biomarkers of Parkinson's disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Blueprint for antimicrobial hit discovery targeting metabolic networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Nutritional systems biology modeling: from molecular mechanisms to physiology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

A consensus protocol for the standardization of cerebrospinal fluid collection and biobanking.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

18O stable isotope labeling in MS-based proteomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Mass spectrometry based targeted protein quantification: methods and applications

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Selected reaction monitoring for quantitative proteomics: a tutorial

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Mathematical modeling of folate metabolism: predicted effects of genetic polymorphisms on mechanisms and biomarkers relevant to carcinogenesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Increase in endoplasmic reticulum stress-related proteins and genes in adipose tissue of obese, insulin-resistant individuals

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Aorta protein networks in marginal and acute zinc deficiency

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Identification of potential serum biomarkers of inflammation and lipid modulation that are altered by fish oil supplementation in healthy volunteers.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Proteomic biomarkers of peripheral blood mononuclear cells obtained from postmenopausal women undergoing an intervention with soy isoflavones

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

The Edinburgh human metabolic network reconstruction and its functional analysis

28 September 2017

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Practical points in urinary proteomics

28 September 2017

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The human peripheral blood mononuclear cell proteome responds to a dietary flaxseed-intervention and proteins identified suggest a protective effect in atherosclerosis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Application of metabolic flux analysis to identify the mechanisms of free fatty acid toxicity to human hepatoma cell line

28 September 2017

1 reference

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Differential protein expression profile in the intestinal epithelium from patients with inflammatory bowel disease

28 September 2017

1 reference

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Two-dimensional gel electrophoresis as tool for proteomics studies in combination with protein identification by mass spectrometry

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Mass spectrometry and protein analysis

28 September 2017

1 reference

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Computational model of in vivo human energy metabolism during semistarvation and refeeding

28 September 2017

1 reference

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Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

28 September 2017

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The Orbitrap: a new mass spectrometer

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Uncovering transcriptional regulation of metabolism by using metabolic network topology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Systems biology and new technologies enable predictive and preventative medicine.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Analysis of the urine proteome in patients with pancreatic ductal adenocarcinoma

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

High-efficiency nano- and micro-HPLC--high-resolution Orbitrap-MS platform for top-down proteomics

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Blood folate status and expression of proteins involved in immune function, inflammation, and coagulation: biochemical and proteomic changes in the plasma of humans in response to long-term synthetic folic acid supplementation.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

The physiologic effects of caloric restriction are reflected in the in vivo adipocyte-enriched proteome of overweight/obese subjects

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Stochastic modelling for quantitative description of heterogeneous biological systems.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Characterization of phosphorylated peptides using traveling wave-based and drift cell ion mobility mass spectrometry

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Evaluation of Urine Proteome Pattern Analysis for Its Potential To Reflect Coronary Artery Atherosclerosis in Symptomatic Patients

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA.

28 November 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Urinary Proteomic Biomarkers in Coronary Artery Disease

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

A mathematical model gives insights into nutritional and genetic aspects of folate-mediated one-carbon metabolism.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Dietary effects of copper and iron deficiency on rat intestine: a differential display proteome analysis.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Effect of high-fat diet on the expression of proteins in muscle, adipose tissues, and liver of C57BL/6 mice

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Interfacing the Orbitrap Mass Analyzer to an Electrospray Ion Source

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Effect of acute zinc depletion on zinc homeostasis and plasma zinc kinetics in men.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125684

Proteomic identification of salivary biomarkers of type-2 diabetes

28 November 2018

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12 December 2020

Simplification of product ion spectra derived from multiply charged parent ions via ion/ion chemistry

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12 December 2020

CILAT--a new reagent for quantitative proteomics

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12 December 2020

Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples

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12 December 2020

Protein quantification in label-free LC-MS experiments

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12 December 2020

Protein and polymer analyses up tom/z 100 000 by laser ionization time-of-flight mass spectrometry

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https://api.crossref.org/works/10.3945%2FAN.111.000554

7 January 2021

Electrospray ion source. Another variation on the free-jet theme

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https://api.crossref.org/works/10.3945%2FAN.111.000554

7 January 2021

Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process

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https://api.crossref.org/works/10.3945%2FAN.111.000554

7 January 2021

Cybernetics / Norbert Wiener. - (11.1948)

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https://api.crossref.org/works/10.3945%2FAN.111.000554

7 January 2021

Identifiers

DOI

10.3945/AN.111.000554

0 references

1 reference

PubMed publication ID

22332076

1 reference