Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags

Dayon, Loı̈c; Pasquarello, Carla; Hoogland, Christine; Sanchez, Jean‐Charles; Scherl, Alexander

doi:10.1016/j.jprot.2009.10.015

Cited by 101 publications

(102 citation statements)

References 19 publications

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“…Liquid Chromatography ESI LTQ-OT MS-ESI LTQ-OT MS was performed as described elsewhere (27). Mass spectra were acquired in the positive mode with an m/z window of 400 -2000 Th.…”

Section: Methodsmentioning

confidence: 99%

Discovery and Verification of Osteopontin and Beta-2-microglobulin as Promising Markers for Staging Human African Trypanosomiasis

Tiberti¹,

Hainard²,

Lejon

et al. 2010

Molecular & Cellular Proteomics

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Human African trypanosomiasis, or sleeping sickness, is a parasitic disease endemic in sub-Saharan Africa, transmitted to humans through the bite of a tsetse fly. The first or hemolymphatic stage of the disease is associated with presence of parasites in the bloodstream, lymphatic system, and body tissues. If patients are left untreated, parasites cross the blood-brain barrier and invade the cerebrospinal fluid and the brain parenchyma, giving rise to the second or meningoencephalitic stage. Stage determination is a crucial step in guiding the choice of treatment, as drugs used for S2 are potentially dangerous. Current staging methods, based on counting white blood cells and demonstrating trypanosomes in cerebrospinal fluid, lack specificity and/or sensitivity. In the present study, we used several proteomic strategies to discover new markers with potential for staging human African trypanosomiasis. Cerebrospinal fluid (CSF) samples were collected from patients infected with Trypanosoma brucei gambiense in the Democratic Republic of Congo. The stage was determined following the guidelines of the national control program. The proteome of the samples was analyzed by two-dimensional gel electrophoresis (n ‫؍‬ 9), and by sixplex tandem mass tag (TMT) isobaric labeling (n ‫؍‬ 6) quantitative mass spectrometry. Overall, 73 proteins were overexpressed in patients presenting the second stage of the disease. Two of these, osteopontin and ␤-2-microglobulin, were confirmed to be potential markers for staging human African trypanosomiasis (HAT) by Western blot and ELISA. The two proteins significantly discriminated between S1 and S2 patients with high sensitivity (68% and 78%, respectively) for 100% specificity, and a combination of both improved the sensitivity to 91%. The levels of osteopontin and ␤-2-microglobulin in CSF of S2 patients (g/ml range), as well as the fold increased concentration in S2 compared with S1 (3.8 and 5.5 respectively) make the two markers good candidates for the development of a test for staging HAT patients. Molecular & Cellular Proteomics 9:2783-2795, 2010.

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“…Liquid Chromatography ESI LTQ-OT MS-ESI LTQ-OT MS was performed as described elsewhere (27). Mass spectra were acquired in the positive mode with an m/z window of 400 -2000 Th.…”

Section: Methodsmentioning

confidence: 99%

Discovery and Verification of Osteopontin and Beta-2-microglobulin as Promising Markers for Staging Human African Trypanosomiasis

Tiberti¹,

Hainard²,

Lejon

et al. 2010

Molecular & Cellular Proteomics

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, since only a tiny fraction of the quantified proteins are usually outside this range (in this data set only 3 of the 3000 quantified S. pombe proteins), their quantities can be manually investigated and verified with relatively little efforts. For samples with strong protein concentration differences, MS methods that increase reporter ion intensities and therefore the overall linear dynamic quantification range should be considered [44,45]. To conclude, the TMT approach presented here was capable of system--wide estimation of protein abundances at accuracies similar to the commonly used LFQ only approaches, even when the sample is extensively fractionated.…”

Section: System--wide Estimation Of Protein Abundances In S Pombementioning

confidence: 87%

Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry

Ahrné

Martínez-Segura

Syed

et al. 2015

Methods

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“…After peak list generation, the CID and HCD spectra were merged for simultaneous identification and quantification [11] (http:// www.expasy.org/tools/HCD_CID_merger.html). The monoisotopic masses of the selected precursor ions were corrected using an in-house written Perl script [12].…”

Section: Database Searchingmentioning

confidence: 99%

Time-course proteomic analysis of taurocholate-induced necrotizing acute pancreatitis

Fétaud-Lapierre

Pastor

Jorge-Costa

et al. 2013

Journal of Proteomics

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Acute pancreatitis is an inflammatory disease of the pancreas, which varies greatly in course and severity. Severe forms are associated with serious local and/or systemic complications, and eventually death. The pathobiology of acute pancreatitis is complex.Animal models have been developed to investigate pathobiological processes and identify factors determining disease course. We performed a time-course proteomic analysis using a rat model of severe necrotizing acute pancreatitis induced by taurocholate perfusion in the pancreatic ducts. Results showed that levels of proteins associated to a given biological process changed in a coordinated fashion after disease onset. It was possible to follow the response of a particular pathobiological process to pancreatitis induction and to compare the course of protein pathways. Proteins involved in acinar cell secretion were found to follow a different kinetics than other cellular processes. After an initial decrease, secretory pathway-associated proteins raised again at 18 h post-induction. This phenomenon coincided with a burst in the expression of pancreatitis-associated protein (REG3A), an acute phase protein produced by the exocrine pancreas, and with the decrease of classical markers of pancreatic injury, suggesting that the expression of proteins associated to the secretory pathway may be a modulating factor of pancreas injury. S 8 5 ( 2 0 1 3 ) 1 2 -2 7Abbreviations: AP, acute pancreatitis; MS, mass spectrometry; MPO, myeloperoxidase; IHC, immunohistochemistry; LACB, bovine ß-lactoglobulin; CV, coefficient of variation; GO, gene ontology; A1I3, alpha-1-inhibitor 3; REG3A, pancreatitis-associated protein 1; GP2, pancreatic secretory granule membrane major glycoprotein; COPD, coatomer delta; COPB, coatomer beta. ☆ This study was supported by grants from the Swiss National Science Foundation no. 320000-120021 and no. 320000-113225/1. by a severe disease with pancreatic necrosis and systemic inflammation. The objectives of this study were to determine the kinetics of functionally related proteins in the early steps of the experimental disease in order to identify protein pathways playing key roles in AP pathobiology and to correlate these data with parameters classically used to assess disease severity. The present work provides for the first time an overview of protein expression in the pancreas during the course of taurocholate-induced necrotizing AP. We believe that correlation of these results with data obtained using proteomic or biochemical approaches in various experimental models of AP will help in highlighting new features, generating hypotheses and constitute therefore a strong and reliable basis for further targeted investigations.

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Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags

Cited by 101 publications

References 19 publications

Discovery and Verification of Osteopontin and Beta-2-microglobulin as Promising Markers for Staging Human African Trypanosomiasis

Discovery and Verification of Osteopontin and Beta-2-microglobulin as Promising Markers for Staging Human African Trypanosomiasis

Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry

Time-course proteomic analysis of taurocholate-induced necrotizing acute pancreatitis

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