scholarly journals Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

2010 ◽  
Vol 28 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Noelle M Griffin ◽  
Jingyi Yu ◽  
Fred Long ◽  
Phil Oh ◽  
Sabrina Shore ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Mass Spectrometry Data ◽  
Label Free ◽  
Complex Mass

scholarly journals Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 836 ◽  
Author(s):  
Jayaseelan Murugaiyan ◽  
Murat Eravci ◽  
Christoph Weise ◽  
Uwe Roesler ◽  
Lisa D. Sprague ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Brucella Melitensis ◽  
Mass Spectrometry Data ◽  
Human Brucellosis ◽  
Label Free ◽  
Natural Hosts ◽  
Causative Agents ◽  
Full Scan ◽  
Gene Ontologies

Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella. The species, B. abortus and B. melitensis, major causative agents of human brucellosis, share remarkably similar genomes, but they differ in their natural hosts, phenotype, antigenic, immunogenic, proteomic and metabolomic properties. In the present study, label-free quantitative proteomic analysis was applied to investigate protein expression level differences. Type strains and field strains were each cultured six times, cells were harvested at a midlogarithmic growth phase and proteins were extracted. Following trypsin digestion, the peptides were desalted, separated by reverse-phase nanoLC, ionized using electrospray ionization and transferred into an linear trap quadrapole (LTQ) Orbitrap Velos mass spectrometer to record full scan MS spectra (m/z 300–1700) and tandem mass spectrometry (MS/MS) spectra of the 20 most intense ions. Database matching with the reference proteomes resulted in the identification of 826 proteins. The Cluster of Gene Ontologies of the identified proteins revealed differences in bimolecular transport and protein synthesis mechanisms between these two strains. Among several other proteins, antifreeze proteins, Omp10, superoxide dismutase and 30S ribosomal protein S14 were predicted as potential virulence factors among the proteins differentially expressed. All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.

scholarly journals Label-Free Liquid Chromatography–Mass Spectrometry Proteomic Analysis of Urinary Identification in Diabetic Vascular Dementia in a Han Chinese Population

2021 ◽  
Vol 13 ◽  
Author(s):  
Ruijuan Chen ◽  
Yuanjing Yi ◽  
Wenbiao Xiao ◽  
Bowen Zhong ◽  
Yi Shu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Vascular Dementia ◽  
Roc Curve ◽  
Proteomic Analysis ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Proteome Discoverer ◽  
Quantitative Changes ◽  
Underlying Mechanisms

Objective: This study aimed to identify potential diagnostic biomarkers of diabetic vascular dementia (DVD) and unravel the underlying mechanisms using mass spectrometry (MS).Methods: Label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic analysis was applied to urine samples from four groups, including 14 patients with vascular dementia (VD), 22 patients with type 2 diabetes mellitus (T2DM), 12 patients with DVD, and 21 normal controls (NCs). Searching the MS data by Proteome Discoverer software (ThermoFisher Scientific; Waltham, MA, USA), protein abundances were analyzed qualitatively and quantitatively and compared between these groups. Combining bioinformatics analysis using Gene Ontology (GO), pathway crosstalk analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG), protein–protein interaction (PPI) network analysis using STRING, and literature searching, the differentially expressed proteins (DEPs) of DVD can be comprehensively judged and were further quantified by receiver operating characteristic (ROC) curve methods.Results: The proteomic findings showed quantitative changes in patients with DVD compared to patients with NC, T2DM, and VD groups; among 4,744 identified urine proteins, 1,222, 1,152, and 1,180 proteins displayed quantitative changes unique to DVD vs. NC, T2DM, and VD, respectively, including 481 overlapped common DEPs. Then, nine unique proteins [including HP, SERPIND, ATP5PB, VNN2, ALDH3A1, U2AF2, C6, A0A5C2GRG5 (no name), and A0A5C2FZ29 (no name)] and two composite markers (CM) (A0A5C2GRG5+U2AF2 and U2AF2+C6) were confirmed by a ROC curve method.Conclusion: This study provided an insight into the potential pathogenesis of DVD and elucidated a method for early detection.

scholarly journals Mass spectrometry data from proteomic analysis of human skin keratins after exposure to UV radiation

Data in Brief ◽  
2016 ◽  
Vol 7 ◽  
pp. 100-106 ◽  
Author(s):  
Seon Hwa Lee ◽  
Keita Matsushima ◽  
Kohei Miyamoto ◽  
Tomoyuki Oe
Keyword(s):  
Mass Spectrometry ◽  
Human Skin ◽  
Uv Radiation ◽  
Proteomic Analysis ◽  
Mass Spectrometry Data

scholarly journals Label-free mass spectrometry-based protein quantification technologies in proteomic analysis

2008 ◽  
Vol 7 (5) ◽  
pp. 329-339 ◽  
Author(s):  
M. Wang ◽  
J. You ◽  
K. G. Bemis ◽  
T. J. Tegeler ◽  
D. P. G. Brown
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Protein Quantification ◽  
Label Free
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