Database search post‐processing by neural network: Advanced facilities for identification of components in protein mixtures using mass spectrometric peptide mapping

Lokhov, Petr G.; Tikhonova, Olga V.; Moshkovskii, Sergei A.; Goufman, Eugene; Серебрякова, М В; Maksimov, B. I.; Toropyguine, I. Yu.; Zgoda, Victor G.; Govorun, Vadim M.; Archakov, Alexander I.

doi:10.1002/pmic.200300580

Cited by 18 publications

(9 citation statements)

References 22 publications

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“…According to Lokhov et al (2004) and Lisitsa et al (2010), a mixture of 2-5 proteins was commonly observed in the SDS-PAGE slice band when analysed using peptide mass fingerprinting. Similar results were also observed by Petushkova et al (2012): separation of protein by SDS-PAGE resulted in more than one protein per gel band.…”

Section: Resultsmentioning

confidence: 99%

Proteomic Analysis of a 14.2 kDa Protein Isolated from Bali Cattle(Bos Sondaicus/Javanicus)Saliva Using Single Dimension Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Tandem Mass Spectrometer

Depamede

2013

Italian Journal of Animal Science

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A 14.2 kDa protein isolated from Bali cattle (Bos sondaicus/javanicus) saliva has been reported to have a bactericidal activity. The aim of this study was to analyse the nature of a 14.2 kDa protein using single dimension (1-D) sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF). The protein was isolated by means of polyethylene glycol (PEG)/sodium sulfate aqueous twophase system, and then determined by 12.5% SDS-PAGE. A band of 14.2 kDa was sliced and analysed by MALDI TOF/TOF mass spectrometer using a 5800 proteomics analyzer. Mascot search and National Center for Biotechnology Information (NCBI) Blast search revealed that the spot of 1-D SDS-PAGE consisted of three proteins: zymogen granule protein 16 homologue B, pancreatic adenocarcinoma upregulated factor-like, and prolactin-inducible protein homologue precursor. The three proteins have been observed in Bos taurus and other species such as mouse. The actual nature of the proteins and their function in Bali cattle (Bos sondaicus/javanicus), as well as the connection with the evolution of bovines need further analysis.

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Section: Resultsmentioning

confidence: 99%

Proteomic Analysis of a 14.2 kDa Protein Isolated from Bali Cattle(Bos Sondaicus/Javanicus)Saliva Using Single Dimension Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Tandem Mass Spectrometer

Depamede

2013

Italian Journal of Animal Science

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“…the SDS-PAGE lane is cut into slices whereupon the protein content of each slice is analyzed by MS method [2,3,7]. Analysis of obtained slices by peptide mass fingerprinting (PMF) has shown that each slice often appears to be a mixture of 2 to 5 proteins [2,10]. Mixed spectra impeded identification, which necessitated the development of additional functions for the software; e.g.…”

Section: Introductionmentioning

confidence: 99%

Optimization of the SDS-PAGE gel slicing approach for identification of human liver microsomal proteins via MALDI-TOF mass spectrometry

Петушкова¹,

Ларіна²,

Chernobrovkin³

et al. 2012

JPB

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Proteomics often exploits sequential cutting of the SDS-PAGE gel lane into slices with subsequent identification of proteins by peptide mass fingerprinting (PMF). In this paper, the influence of slice thickness on protein identification was investigated. Following the separation of the human liver microsomal fraction, the 37 to 75 kDa range of the gel lane was cut into 20 or 40 slices of 0.5 mm and 0.25 mm thickness, respectively. Identification of proteins after trypsinolysis was performed by MALDI-TOF mass spectrometry. A twofold reduction of slice thickness did not influence the number of peaks in PMF-spectra. It was established that at a tolerance of 0.15 Da the number of identified proteins in the 40 slices series exceeded by more than twofold the number of identifications in 20 slices series. It was shown that the decrease of slice thickness leads to a considerable enhancement of peptide peak's intensity and, also, to the changes of PMF-spectra which resulted gaining additional peptides for enrichment of sequence coverage.

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“…The probability of identification was shown by the MOWSE score [20] and the sequence alignment was achieved by the T-COFFEE program [21]. …”

Section: Methodsmentioning

confidence: 99%

Severe Immediate Allergic Reactions to Grapes: Part of a Lipid Transfer Protein-Associated Clinical Syndrome

Vassilopoulou

Zuidmeer

Akkerdaas

et al. 2007

Int Arch Allergy Immunol

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Background: Grape allergy is considered rare; grape lipid transfer protein (LTP; Vit v 1), an endochitinase and a thaumatin-like protein (TLP) have been reported as grape allergens. A considerable number of patients have referred to our department for severe reactions to grapes, and several IgE binding proteins were detected. Objectives: The aim of this study was to identify and characterise the allergens involved in severe allergic reactions to grapes and describe the population in which they occur. Methods: Patients with reported severe allergic reactions to grapes (n = 37) are described. Grape allergens were purified/fractionated by a combination of chromatographic techniques, identified by proteomic analysis and biochemically characterised. Immunoreactivity was assessed by blot (inhibitions) and RAST (inhibitions), and skin prick tests were performed with the isolated allergens. Results: All subjects were polyallergic, sensitised and reactive to several additional foods and pollen. All patients were sensitised to grape LTP. A 28-kDa expansin, a 37.5-kDa polygalacturonase-inhibiting protein, a 39-kDa β-1,3-glucanase and a 60-kDa protein were identified as minor grape allergens. Endochitinase and TLP did not play a role. Inhibition experiments revealed the possible cross-reactive role of LTP for clinical sensitivities to other LTP-containing plant foods, but also the involvement of cross-reactive carbohydrate determinants of minor allergens in IgE cross-reactivity. Conclusions: LTP is the major grape allergen, while additional minor allergens may contribute to clinical reactivity. Severe grape allergy presents in atopic patients who frequently react to other LTP-containing, plant-derived foods. The ‘LTP syndrome’ is the appropriate term to describe this condition.

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Database search post‐processing by neural network: Advanced facilities for identification of components in protein mixtures using mass spectrometric peptide mapping

Cited by 18 publications

References 22 publications

Proteomic Analysis of a 14.2 kDa Protein Isolated from Bali Cattle(Bos Sondaicus/Javanicus)Saliva Using Single Dimension Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Tandem Mass Spectrometer

Proteomic Analysis of a 14.2 kDa Protein Isolated from Bali Cattle(Bos Sondaicus/Javanicus)Saliva Using Single Dimension Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Tandem Mass Spectrometer

Optimization of the SDS-PAGE gel slicing approach for identification of human liver microsomal proteins via MALDI-TOF mass spectrometry

Severe Immediate Allergic Reactions to Grapes: Part of a Lipid Transfer Protein-Associated Clinical Syndrome

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