scholarly journals Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis

2015 ◽  
Vol 55 (2) ◽  
pp. 219-230 ◽  
Author(s):  
Truong Quoc Phong ◽  
Do Thi Thu Ha ◽  
Uwe Volker ◽  
Elke Hammer
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Quantitative Proteomics ◽  
Multidrug Resistant ◽  
Protein Abundance ◽  
Label Free ◽  
Proteomics Approach

scholarly journals Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 607
Author(s):  
Nadeem Ullah ◽  
Ling Hao ◽  
Jo-Lewis Banga Ndzouboukou ◽  
Shiyun Chen ◽  
Yaqi Wu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Control Strategies ◽  
Multidrug Resistant ◽  
Differentially Expressed ◽  
Effective Control ◽  
Drug Resistant ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Candidate Target

Rifampicin (RIF) is one of the most important first-line anti-tuberculosis (TB) drugs, and more than 90% of RIF-resistant (RR) Mycobacterium tuberculosis clinical isolates belong to multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. In order to identify specific candidate target proteins as diagnostic markers or drug targets, differential protein expression between drug-sensitive (DS) and drug-resistant (DR) strains remains to be investigated. In the present study, a label-free, quantitative proteomics technique was performed to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41 proteins were not detected in the DS strain. Functional category showed that these differentially expressed proteins were mainly involved in the cell wall and cell processes. When compared to the RR strain, Rv2272, smtB, lpqB, icd1, and folK were up-regulated, while esxK, PPE19, Rv1534, rpmI, ureA, tpx, mpt64, frr, Rv3678c, esxB, esxA, and espL were down-regulated in both MDR and XDR strains. Additionally, nrp, PPE3, mntH, Rv1188, Rv1473, nadB, PPE36, and sseA were specifically expressed in both MDR and XDR strains, whereas 292 proteins were not identified when compared to the RR strain. When compared between MDR and XDR strains, 52 proteins were up-regulated, while 45 proteins were down-regulated in the XDR strain. 316 proteins were especially expressed in the XDR strain, while 92 proteins were especially detected in the MDR strain. Protein interaction networks further revealed the mechanism of their involvement in virulence and drug resistance. Therefore, these differentially expressed proteins are of great significance for exploring effective control strategies of DR-TB.

scholarly journals Drafting the CLN3 Protein Interactome in SH-SY5Y Human Neuroblastoma Cells: A Label-free Quantitative Proteomics Approach

2013 ◽  
Vol 12 (5) ◽  
pp. 2101-2115 ◽  
Author(s):  
Enzo Scifo ◽  
Agnieszka Szwajda ◽  
Janusz Dębski ◽  
Kristiina Uusi-Rauva ◽  
Tapio Kesti ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Neuroblastoma Cells ◽  
Label Free ◽  
Human Neuroblastoma Cells ◽  
Human Neuroblastoma ◽  
Protein Interactome ◽  
Proteomics Approach

scholarly journals Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3591
Author(s):  
Pratiti Bhadra ◽  
Stefan Schorr ◽  
Monika Lerner ◽  
Duy Nguyen ◽  
Johanna Dudek ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Secretory Pathway ◽  
Human Cells ◽  
Ribosome Profiling ◽  
Protein Abundance ◽  
Label Free ◽  
Differential Protein ◽  
Cellular Assays ◽  
Pros And Cons ◽  
Er Membrane

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.

scholarly journals Novel MMP-9 Substrates in Cancer Cells Revealed by a Label-free Quantitative Proteomics Approach

2008 ◽  
Vol 7 (11) ◽  
pp. 2215-2228 ◽  
Author(s):  
Danmei Xu ◽  
Naoko Suenaga ◽  
Mariola J. Edelmann ◽  
Rafael Fridman ◽  
Ruth J. Muschel ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Quantitative Proteomics ◽  
Label Free ◽  
Proteomics Approach

Identification of novel ADAMTS1, ADAMTS4 and ADAMTS5 cleavage sites in versican using a label-free quantitative proteomics approach

2021 ◽  
Vol 249 ◽  
pp. 104358
Author(s):  
Daniel R. Martin ◽  
Salvatore Santamaria ◽  
Christopher D. Koch ◽  
Josefin Ahnström ◽  
Suneel S. Apte
Keyword(s):  
Quantitative Proteomics ◽  
Cleavage Sites ◽  
Label Free ◽  
Proteomics Approach

Correction to Drafting the CLN3 Protein Interactome in SH-SY5Y Human Neuroblastoma Cells: A Label-free Quantitative Proteomics Approach

2013 ◽  
Vol 12 (8) ◽  
pp. 3822-3822
Author(s):  
Enzo Scifo ◽  
Agnieszka Szwajda ◽  
Janusz Dębski ◽  
Kristiina Uusi-Rauva ◽  
Tapio Kesti ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Neuroblastoma Cells ◽  
Label Free ◽  
Human Neuroblastoma Cells ◽  
Human Neuroblastoma ◽  
Protein Interactome ◽  
Proteomics Approach

Abstract 4533: Mechanism of anti-proliferative effects of sanguinarine in pancreatic cancer cells: A label-free quantitative proteomics approach

2014 ◽  
Author(s):  
Chandra K. Singh ◽  
Satwinderjeet Kaur ◽  
Jasmine George ◽  
Molly C. Pellitteri-Hahn ◽  
Cameron O. Scarlett ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cancer Cells ◽  
Quantitative Proteomics ◽  
Label Free ◽  
Pancreatic Cancer Cells ◽  
Proteomics Approach

scholarly journals Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Cosette Abdallah ◽  
Eliane Dumas-Gaudot ◽  
Jenny Renaut ◽  
Kjell Sergeant
Keyword(s):  
Quantitative Proteomics ◽  
Protein Extraction ◽  
State Of The Art ◽  
Rapid Expansion ◽  
Protein Abundance ◽  
Label Free ◽  
Genome Sequences ◽  
Two Dimensional Gel Electrophoresis ◽  
Green Tissue ◽  
Peptide Fractionation

Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.

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