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1.
J Chromatogr A ; 1628: 461443, 2020 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-32822982

RESUMO

Sodium dodecyl sulfate (SDS) in proteomics samples needs to be removed and estimated prior to mass spectrometry (MS)-based analysis and to avoid MS ion-source contamination. Here, we describe an organic solvent free method to remove SDS using a simple apparatus that mainly consists of an agarose gel inside a 1 mL plastic micropipette tip and a voltage power supply with electrodes. A small volume of sample (e.g., 50 µL) is loaded on top of the gel and then voltage (cathode at the sample side) is applied with an acidic solution at the other end of the micropipette tip. Within 25 min, SDS was removed (e.g., ≥99% SDS in 3.5 mM SDS) and the peptides were retained in the sample solution. The strategy was compared to the commercially available and expensive Pierce spin column for the removal of SDS and recovery of peptides from a digested bovine serum albumin sample.


Assuntos
Técnicas de Química Analítica/métodos , Técnicas Eletroquímicas , Proteômica/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Eletroforese em Gel de Poliacrilamida , Espectrometria de Massas , Peptídeos/química , Soroalbumina Bovina/química , Dodecilsulfato de Sódio/química
2.
J Oleo Sci ; 69(1): 65-72, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31902896

RESUMO

The secondary structures of human serum albumin (HSA) and bovine serum albumin (BSA) were disrupted in the solution of sodium dodecyl sulfate (SDS), while being hardly damaged in the solution of the bile salt, sodium cholate (NaCho). In the present work, the removal of dodecyl sulfate (DS) ions bound to these proteins was attempted by adding various amounts of NaCho. The extent of removal was estimated by the restoration of α-helical structure of each protein disrupted by SDS. Increases and decreases in α-helical structure were examined using the mean residue ellipticity at 222 nm, [θ]222, which was frequently used as a measure of α-helical structure content. The magnitudes of [θ]222 of HSA and BSA, weakened by SDS, were restrengthened upon the addition of NaCho. This indicated that the α-helical structures of HSA and BSA that were disrupted by the binding of DS ions were nearly reformed by the addition of NaCho. The NaCho concentration at which the maximum restoration of [θ]222 of each protein was attained increased nearly linearly with SDS concentration. These results indicated that most of the bound DS ions were removed from the proteins but the removal was incomplete. The removal of DS ions, examined by means of the equilibrium dialysis, was also incomplete. The α-helical structure restoration and the DS ion removal by NaCho were considered to be due to the ability of cholate anions to strip the surfactant ions bound to HSA and BSA. These stripped DS ions appeared to be more likely to form SDS-NaCho mixed micelles in bulk rather than SDS-NaCho mixed aggregates on the proteins.


Assuntos
Soroalbumina Bovina/química , Albumina Sérica/química , Colato de Sódio/química , Dodecilsulfato de Sódio/isolamento & purificação , Tensoativos/isolamento & purificação , Animais , Bovinos , Humanos , Ligação Proteica , Psicoterapia Breve , Dodecilsulfato de Sódio/química , Tensoativos/química
3.
Methods Mol Biol ; 1855: 479-482, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30426441

RESUMO

Protein gel electrophoresis is an important procedure carried out in protein studies. Elution and recovery of proteins separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) are often necessary for further downstream analyses. The process involves localizing the protein of interest on the gel following SDS-PAGE, eluting the protein from the gel, removing SDS from the eluted sample, and finally renaturing the protein (e.g., enzymes) for subsequent analyses. Investigators have extracted proteins from gels by a variety of techniques. These include dissolution of the gel matrix, passive diffusion, and electrophoretic elution. Proteins eluted from gels have been used successfully in a variety of downstream applications, including protein chemistry, proteolytic cleavage, determination of amino acid composition, polypeptide identification by trypsin digestion and matrix-assisted laser desorption ionization-time of flight mass spectroscopy, as antigens for antibody production, identifying a polypeptide corresponding to an enzyme activity, and other purposes. Protein yields ranging from nanogram levels to 100 µg have been obtained. Here, we review some of the methods that have been used to elute proteins from gels.


Assuntos
Eletroforese em Gel de Poliacrilamida/métodos , Proteínas/isolamento & purificação , Animais , Difusão , Eletroforese em Gel de Poliacrilamida/instrumentação , Géis/química , Humanos , Desnaturação Proteica , Dodecilsulfato de Sódio/isolamento & purificação
4.
Anal Chem ; 90(17): 10122-10127, 2018 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-30074774

RESUMO

The removal of sodium dodecyl sulfate (SDS) in SDS-assisted proteomics with electrospray-ionization-mass-spectrometric (ESI-MS) analysis is an essential step in the analysis. Off-line state-of-the-art sample-preparation strategies can allow 100% removal of DS- and up to 100% peptide recoveries. These strategies, however, are typically laborious and require long analysis times and a complex experimental setup. Here, we developed a simple, membrane-free, electrokinetic, on-line, integrated SDS removal-ESI-MS device that was able to enhance ESI-MS signals of bradykinin and peptides from trypsin-digested bovine serum albumin (BSA) in samples that contained SDS micelles. The significant peptide-signal improvements were contributed by the complete removal of DS- and the enrichment of the peptides in the presence of an electric field. Enrichment was via micelle-to-solvent stacking, initially developed in capillary electrophoresis. Bradykinin percent recovery was 800%, and BSA peptide percent recovery was 87%. Enhancement factors in ESI-MS signals (after and before removal) for selected m/ z values of peptides from the BSA digest were 535-693.


Assuntos
Peptídeos/química , Dodecilsulfato de Sódio/isolamento & purificação , Espectrometria de Massas por Ionização por Electrospray/instrumentação , Bradicinina/química , Eletroforese Capilar , Estudo de Prova de Conceito , Proteômica , Soroalbumina Bovina/química , Espectrometria de Massas por Ionização por Electrospray/métodos , Tripsina/química
5.
J Proteome Res ; 17(7): 2390-2400, 2018 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-29888605

RESUMO

Biological research often requires the use of sodium dodecyl sulfate (SDS) to solubilize protein samples; however, this detergent is not compatible with direct mass spectrometry (MS) analysis. Here, we report an online high-throughput proteomics method that permits standard in-solution digestion of SDS-containing samples followed by direct liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analysis using weak cation-exchange chromatography (WCX). This approach, called the online removal of sodium dodecyl sulfate (Online reSDS), exploits the properties of WCX in a highly organic and mildly acidic medium to retain positively charged peptides by both hydrophilic interaction and electrostatic attraction while simultaneously repelling negative SDS molecules. This method was optimized to successfully analyze complex samples that contain up to 1% of SDS. Furthermore, online reSDS improves the identification of peptides with post-translational modifications (PTMs), such as deamidation and phosphorylation, without preliminary enrichment. In conclusion, we show that reSDS can facilitate research in proteomics by allowing the use of SDS in a wide range of LC-MS/MS applications with simplified sample-processing procedures.


Assuntos
Cromatografia por Troca Iônica/métodos , Peptídeos/análise , Dodecilsulfato de Sódio/isolamento & purificação , Cromatografia Líquida , Interações Hidrofóbicas e Hidrofílicas , Métodos , Proteômica/métodos , Eletricidade Estática , Espectrometria de Massas em Tandem
6.
Anal Chim Acta ; 1005: 54-60, 2018 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-29389319

RESUMO

Sodium dodecyl sulfate (SDS) removal is a vital procedure in SDS-assisted bottom-up proteomics because SDS affects the quality of the data in electrospray ionization mass spectrometry (ESI-MS). SDS removal methods provide efficient removal of SDS and improved peptide analysis, but would usually require time, specialised devices, and experienced analysts. Here, by simple addition of γ-cyclodextrin (γ-CD) to the solution at concentrations 1 to 2x the SDS in the sample, the SDS related signals in positive ionization ESI-MS can be significantly removed (70-99% reduction), without an additional sample manipulation step of extraction or purification. The mechanism for removal is based on the formation of tightly bound CD-SDS inclusion complexes, which hampered the generation of positively charged SDS multimers during ESI. For a sample with peptides (glu-val-phe, tyr-tyr-tyr, and bradykinin) and 3 mM SDS where 6 mM γ-CD was added, the %signal recoveries of peptides calculated by comparison with signals from standard samples without SDS were 49-59%. The space charge effect by SDS on bradykinin was also reduced, increasing the signal for bradykinin 12x in the presence of γ-CD. For a protein (bovine serum albumin, BSA) digest with 3 mM SDS, which is an expected concentration in trypsin treated samples, a noticeable 7-fold improvement in the peptide to SDS signal ratio and a 91% reduction of SDS signals were observed upon addition of 6 mM γ-CD. However, there were only small changes in the ESI-MS intensities for the BSA peptides (compared to without addition of γ-CD). This new approach to SDS signal removal using CDs in ESI-MS may find use in proteomic studies.


Assuntos
Detergentes/isolamento & purificação , Peptídeos/análise , Dodecilsulfato de Sódio/isolamento & purificação , Espectrometria de Massas por Ionização por Electrospray/métodos , gama-Ciclodextrinas/química , Animais , Bradicinina/análise , Bovinos , Soroalbumina Bovina/química
7.
Electrophoresis ; 39(11): 1349-1356, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29417596

RESUMO

SDS plays a key role in proteomics workflows, including protein extraction, solubilization and mass-based separations (e.g. SDS-PAGE, GELFrEE). However, SDS interferes with mass spectrometry and so it must be removed prior to analysis. We recently introduced an electrophoretic platform, termed transmembrane electrophoresis (TME), enabling extensive depletion of SDS from proteins in solution with exceptional protein yields. However, our prior TME runs required 1 h to complete, being limited by Joule heating which causes protein aggregation at higher operating currents. Here, we demonstrate effective strategies to maintain lower TME sample temperatures, permitting accelerated SDS depletion. Among these strategies, the use of a magnetic stir bar to continuously agitate a model protein system (BSA) allows SDS to be depleted below 100 ppm (>98% removal) within 10 min of TME operations, while maintaining exceptional protein recovery (>95%). Moreover, these modifications allow TME to operate without any user intervention, improving throughput and robustness of the approach. Through fits of our time-course SDS depletion curves to an exponential model, we calculate SDS depletion half-lives as low as 1.2 min. This promising electrophoretic platform should provide proteomics researchers with an effective purification strategy to enable MS characterization of SDS-containing proteins.


Assuntos
Eletroforese/métodos , Proteínas/isolamento & purificação , Dodecilsulfato de Sódio/isolamento & purificação , Calefação , Espectrometria de Massas , Proteômica/métodos , Fatores de Tempo
8.
Anal Chem ; 89(24): 13058-13063, 2017 12 19.
Artigo em Inglês | MEDLINE | ID: mdl-29154539

RESUMO

In proteomics, dodecyl sulfate (DS-) as sodium salt is commonly used in protein solubilization prior to tryptic digestion, but the presence of the DS- hampers the electrospray ionization mass spectrometric (ESI-MS) analysis. The development of DS- depletion techniques is therefore important especially when dealing with small samples where there could be poor sensitivity due to sample loss or dilution during sample preparation. Here, we present a simple and fast electrokinetic removal method of DS- from small volumes of peptide and digested protein samples prior to ESI-MS. The selective removal was accomplished using an acidic extraction solution (ES) containing acetonitrile (ACN) inside a fused-silica capillary that was dipped into the sample. The use of acidic ES suppressed the electroosmotic flow; allowing the electrokinetic movement of DS- monomers and micelles into the capillary. The high amount of ACN present at the tip of the capillary served to collapse the micelles migrating into the capillary, thereby releasing the peptides that were bound to these micelles, facilitating peptide retention in the sample and efficient DS- removal. Increased % MS signal intensity (SI) restoration of the peptide was observed, while DS- removal was unaffected when the amount of ACN in the ES was increased. This is because of the micelle to solvent stacking mechanism (effective electrophoretic mobility reversal) working at high concentration of ACN for the improved recovery of the peptides. % MS SI restoration for the Z-Gly-Gly-Val and bradykinin peptides were 75-83% while % MS SI reduction of DS- was up to 99% under optimal conditions, that is, 40% ACN in the ES. Higher % peptide recoveries from digested protein samples were obtained using the proposed method compared to the conventional cold acetone precipitation method.


Assuntos
Bradicinina/análise , Conalbumina/química , Concanavalina A/química , Eletro-Osmose , Micelas , Soroalbumina Bovina/química , Dodecilsulfato de Sódio/isolamento & purificação , Acetonitrilas/química , Animais , Bovinos , Peptídeos/análise , Dodecilsulfato de Sódio/química , Espectrometria de Massas por Ionização por Electrospray
9.
Electrophoresis ; 38(7): 1044-1052, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28008632

RESUMO

Capillary electrophoresis is an important technique for the characterization of monoclonal antibodies (mAbs), especially in the pharmaceutical context. However, identification is difficult as upscaling and hyphenation of used methods directly to mass spectrometry is often not possible due to separation medium components that are incompatible with MS detection. Here a CE-MS method for the analysis of mAbs is presented analyzing SDS-complexed samples. To obtain narrow and intensive peaks of SDS-treated antibodies, an in-capillary strategy was developed based on the co-injection of positively charged surfactants and methanol as organic solvent. For samples containing 0.2% (v/v) of SDS, recovered MS peak intensities up to 97 and 95% were achieved using cetyltrimethylammonium bromide or benzalkonium chloride, respectively. Successful removal of SDS was shown in neutral coated capillaries but also in a capillary with a positively charged coating applying reversed polarity. The usefulness of this in-capillary strategy was demonstrated also for other proteins and for antibodies dissolved in up to 10% v/v SDS solution, and in other SDS-containing matrices, including the sieving matrix used in a standard CE-SDS method and gel-buffers applied in SDS-PAGE methods. The developed CE-MS approaches enable fast and reproducible characterization of SDS-complexed antibodies.


Assuntos
Anticorpos Monoclonais/análise , Eletroforese Capilar/métodos , Espectrometria de Massas/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Reprodutibilidade dos Testes , Dodecilsulfato de Sódio/química
10.
J Proteome Res ; 15(8): 2634-42, 2016 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-27376408

RESUMO

Membrane proteins are underrepresented in proteome analysis platforms because of their hydrophobic character, contributing to decreased solubility. Sodium dodecyl sulfate is a favored denaturant in proteomic workflows, facilitating cell lysis and protein dissolution; however, SDS impedes MS detection and therefore must be removed prior to analysis. Although strategies exist for SDS removal, they provide low recovery, purity, or reproducibility. Here we present a simple automated device, termed transmembrane electrophoresis (TME), incorporating the principles of membrane filtration, but with an applied electric current to ensure near-complete (99.9%) removal of the surfactant, including protein-bound SDS. Intact proteins are recovered in solution phase in high yield (90-100%) within 1 h of operation. The strategy is applied to protein standards and proteome mixtures, including an enriched membrane fraction from E. coli, resulting in quality MS spectra free of SDS adducts. The TME platform is applicable to both bottom-up MS/MS as well as LC-ESI-MS analysis of intact proteins. SDS-depleted fractions reveal a similar number of protein identifications (285) compared wit a non-SDS control (280), being highly correlated in terms of protein spectral counts. This fully automated approach to SDS removal presents a viable tool for proteome sample processing ahead of MS analysis. Data are available via ProteomeXchange, identifier PXD003941.


Assuntos
Eletroforese em Gel de Poliacrilamida/métodos , Proteínas de Membrana/análise , Proteoma/análise , Proteômica/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Automação , Cromatografia Líquida , Escherichia coli , Proteínas de Escherichia coli/análise , Espectrometria de Massas/métodos , Proteoma/normas , Solubilidade , Espectrometria de Massas em Tandem
11.
Rapid Commun Mass Spectrom ; 30(6): 698-704, 2016 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-26864522

RESUMO

RATIONALE: Sodium dodecyl sulfate (SDS) is widely used for the solubilization and denaturation of proteins, but it interferes with liquid chromatography/mass spectrometry (LC/MS), suppressing protein signals or forming adduct ions. A quick and effective clean-up technique of SDS is essential for MS analysis of proteins. Ion-exchange spin columns are commonly used for SDS removal in protein samples. METHODS: A bulk sample of insoluble, cross-linked [Os(dimethylbipyridine)2 Cl](+/2+) -derivatized poly(acrylamide)-poly(vinylimidazole) copolymer was synthesized and broken into small particles. The polymer was activated by washing with 1:1 ACN/water 50 mM triethylammonium phosphate 0.05% TFA, 0.1% TFA ACN and then 0.1% TFA water. Under acidic aqueous conditions, SDS adsorbs on the activated surfaces of the Os-complexed copolymer particles, but not the proteins and peptides in the same mixtures. Thus, the copolymer can be used to remove SDS from protein and peptide samples. The copolymer-adsorbed SDS is removed by washing with 0.1% TFA ACN, permitting re-use of the copolymer. RESULTS: Standard myoglobin and some practical protein samples from a biochemistry lab spiked with different concentrations of SDS were successfully cleaned up using this Os-copolymer for LC/MS analyses. Up to 0.2% (w/v %) of SDS can be successfully removed from those protein samples. CONCLUSIONS: This Os-complexed copolymer provides a new alternative for quick cleanup of SDS from protein samples, and can serve as a new class of metal complex based anion exchanger for protein purification.


Assuntos
2,2'-Dipiridil/química , Acrilamida/química , Imidazóis/química , Osmio/química , Proteínas/análise , Dodecilsulfato de Sódio/isolamento & purificação , Cromatografia Líquida/métodos , Espectrometria de Massas/métodos , Compostos Organometálicos/química , Peptídeos/análise , Peptídeos/química , Proteínas/química , Dodecilsulfato de Sódio/química
12.
Talanta ; 141: 235-8, 2015 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-25966408

RESUMO

In this work, a novel integrated sample preparation device for SDS-assisted proteome analysis was developed, by which proteins dissolved in 4% (w/v) SDS were first diluted by 50% methanol, and then SDS was online removed by a hollow fiber membrane interface (HFMI) with 50mM ammonium bicarbonate (pH 8.0) as an exchange buffer, finally digested by an immobilized enzyme reactor (IMER). To evaluate the performance of such an integrated device, bovine serum albumin dissolved in 4% (w/v) SDS as a model sample was analyzed; it could be found that similar to that obtained by direct analysis of BSA digests without SDS (the sequence coverage of 60.3±1.0%, n=3), with HFMI as an interface for SDS removal, BSA was identified with the sequence coverage of 61.0±1.0% (n=3). However, without SDS removal by HFMI, BSA could not be digested by the IMER and none peptides could be detected. In addition, such an integrated sample preparation device was also applied for the analysis of SDS extracted proteins from rat brain, compared to those obtained by filter-aided sample preparation (FASP), not only the identified protein group and unique peptide number were increased by 12% and 39% respectively, but also the sample pretreatment time was shortened from 24h to 4h. All these results demonstrated that such an integrated sample preparation device would provide an alternative tool for SDS assisted proteome analysis.


Assuntos
Proteínas/análise , Proteômica/instrumentação , Proteômica/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Animais , Química Encefálica , Enzimas Imobilizadas/química , Enzimas Imobilizadas/metabolismo , Desenho de Equipamento , Membranas Artificiais , Sistemas On-Line , Ratos , Soroalbumina Bovina/análise , Soroalbumina Bovina/química , Espectrometria de Massas em Tandem , Tripsina/química , Tripsina/metabolismo
13.
J Proteome Res ; 14(5): 2199-206, 2015 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-25836738

RESUMO

A fractionation method called gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) has been used to dramatically increase the number of proteins identified in top-down proteomic workflows; however, the technique involves the use of sodium dodecyl sulfate (SDS), a surfactant that interferes with electrospray ionization. Therefore, an efficient removal of SDS is absolutely required prior to mass analysis. Traditionally, methanol/chloroform precipitation and spin columns have been used, but they lack reproducibility and are difficult to automate. Therefore, we developed an in-line matrix removal platform to enable the direct analysis of samples containing SDS and salts. Only small molecules like SDS permeate a porous membrane and are removed in a manner similar to cross-flow filtration. With this device, near-complete removal of SDS is accomplished within 5 min and proteins are subsequently mobilized into a mass spectrometer. The new platform was optimized for the analysis of GELFrEE fractions enriched for histones extracted from human HeLa cells. All four core histones and their proteoforms were detected in a single spectrum by high-resolution mass spectrometry. The new method versus protein precipitation/resuspension showed 2- to 10-fold improved signal intensities, offering a clear path forward to improve proteome coverage and the efficiency of top-down proteomics.


Assuntos
Eletroforese/instrumentação , Histonas/isolamento & purificação , Dodecilsulfato de Sódio/isolamento & purificação , Espectrometria de Massas por Ionização por Electrospray/métodos , Calibragem , Eletroforese/métodos , Células HeLa , Humanos , Membranas Artificiais , Porosidade , Isoformas de Proteínas/isolamento & purificação , Padrões de Referência , Dodecilsulfato de Sódio/química
14.
J Histochem Cytochem ; 62(7): 519-31, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24794148

RESUMO

Inconsistent results obtained with published methods for the elution of antibodies from tissue sections prompted the assessment of both old and new methods in combination with monoclonal rabbit antibodies of known, increased affinity (above 1×10(-9) KD). We tested an acidic (pH 2) glycine buffer, a 6 M urea hot buffer and a 2-Mercaptoethanol, SDS buffer (2-ME/SDS). Some antibodies were not removed by the glycine pH 2 or 6 M urea hot buffers, indicating that antibodies survive much harsher conditions than previously believed. We found that the elution is dependent upon the antibody affinity and is reduced by species-specific crosslinking via a dimeric or Fab fragments of a secondary antibody. The high affinity bond of exogenous streptavidin with the endogenous biotin can be removed by 6 M urea but not by the other buffers. 2-ME/SDS buffer is superior to glycine pH 2 and 6 M urea hot elution buffers for all antibodies because of its irreversible effect on the structure of the antibodies. It also has a mild retrieving effect on some antigens present on routinely treated sections and no detrimental effect on the immunoreactivity of the tissue. Therefore, 2-ME/SDS buffer is the method of choice to perform multiple rounds of immunostaining on a single routine section.


Assuntos
Anticorpos Monoclonais/isolamento & purificação , Animais , Soluções Tampão , Fixadores , Formaldeído , Trato Gastrointestinal/química , Humanos , Concentração de Íons de Hidrogênio , Imuno-Histoquímica/métodos , Rim/química , Mercaptoetanol/isolamento & purificação , Tonsila Palatina/química , Inclusão em Parafina , Pele/química , Dodecilsulfato de Sódio/isolamento & purificação , Coloração e Rotulagem/métodos
15.
Proteomics ; 14(2-3): 196-201, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24272977

RESUMO

In-gel digestion followed by LC/MS/MS is widely used for the identification of trace amounts of proteins and for the site-specific glycosylation analysis of glycoproteins in cells and tissues. A major limitation of this technique is the difficulty in acquiring reliable mass spectra for peptides present in minute quantities and glycopeptides with high heterogeneity and poor hydrophobicity. It is considered that the SDS used in electrophoresis can interact with proteins noncovalently and impede the ionization of peptides/glycopeptides. In this study, we report an improved in-gel digestion method to acquire reliable mass spectra of a trace amount of peptides/glycopeptides. A key innovation of our improved method is the use of guanidine hydrochloride, which forms complexes with the residual SDS molecules in the sample. The precipitation and removal of SDS by addition of the guanidine hydrochloride was successful in improving the S/N of peptides/glycopeptides in mass spectra and acquiring a more comprehensive MS/MS data set for the various glycoforms of each glycopeptide.


Assuntos
Eletroforese em Gel de Poliacrilamida/métodos , Glicopeptídeos/química , Glicoproteínas/química , Guanidina/química , Dodecilsulfato de Sódio/química , Sequência de Aminoácidos , Precipitação Química , Cromatografia Líquida/métodos , Glicosilação , Dados de Sequência Molecular , Proteômica/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Espectrometria de Massas em Tandem/métodos
16.
Proteomics ; 12(21): 3138-42, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-22936678

RESUMO

While the use of detergents is necessary for a variety of protein isolation preparation protocols, they are not compatible with mass spectral analysis due to ion suppression and adduct formation. This manuscript describes optimization of detergent removal, using commercially available SDS depletion spin columns containing an affinity resin, providing for both increased protein recovery and thorough SDS removal. Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) allowed for a concurrent analysis of both analyte and detergent. In the case of both proteins and peptides, higher detergent concentrations than previously reported provided an increase of sample recovery; however there was a limit as SDS was detected by IMS-MS at higher levels of SDS indicating incomplete detergent depletion. The results also suggest that optimal conditions for SDS removal are dependent on the sample concentration. Overall, this study provides a useful guide for proteomic studies where SDS is required for efficient sample preparation.


Assuntos
Proteômica/métodos , Dodecilsulfato de Sódio/química , Espectrometria de Massas em Tandem/métodos , Proteínas de Bactérias/química , Modelos Químicos , Fragmentos de Peptídeos/análise , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/isolamento & purificação , Shewanella/química , Dodecilsulfato de Sódio/análise , Dodecilsulfato de Sódio/isolamento & purificação , Ubiquitina/química
17.
Anal Chem ; 84(6): 2862-7, 2012 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-22339560

RESUMO

Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for biological sample extraction; however, the presence of this reagent in samples challenges LC-MS-based proteomics analyses because it can interfere with reversed-phase LC separations and electrospray ionization. This study reports a simple SDS-assisted proteomics sample preparation method facilitated by a novel peptide-level SDS removal step. In an initial demonstration, SDS was effectively (>99.9%) removed from peptide samples through ion substitution-mediated DS(-) precipitation using potassium chloride (KCl), and excellent peptide recovery (>95%) was observed for <20 µg of peptides. Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage obtained for both mammalian tissues and bacterial samples was comparable to or better than that obtained for the same sample types prepared using standard proteomics preparation methods and analyzed using LC-MS/MS. These results suggest the SDS-assisted protocol is a practical, simple, and broadly applicable proteomics sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.


Assuntos
Precipitação Fracionada/métodos , Proteoma/análise , Proteômica/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Espectrometria de Massas em Tandem/métodos , Animais , Proteínas de Bactérias/análise , Proteínas de Bactérias/isolamento & purificação , Cromatografia Líquida/métodos , Peptídeos/análise , Peptídeos/isolamento & purificação , Proteoma/isolamento & purificação , Shewanella/química , Dodecilsulfato de Sódio/química
18.
Electrophoresis ; 33(2): 316-24, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22222976

RESUMO

SDS is mostly used to enhance the solubilization and extraction of membrane proteins due to its strong detergency and low cost. Nevertheless, SDS interferes with the subsequent procedures and needs to be removed from the samples. In this work, a special gradient gel electrophoresis (GGE) system was developed to remove SDS from the SDS-solubilized protein samples. As a proof-of-principle experiment, the GGE system was designed to be composed of an agarose loading layer, six polyacrylamide fractionation layers with different concentrations and a high-concentration polyacrylamide sealing layer. The advantages of the GGE system are that it not only can electrophoretically remove SDS efficiently so that the protein loss resulted from the repeated gel washing after electrophoresis was avoided, but also can reduce the complexity of the sample, prevent the precipitation of proteins after loading and avoid the loss of proteins with low molecular weight during the electrophoresis. Using GGE system, about 85% of SDS in the sample and gel was electrophoretically removed and the proteins were fractionated. Compared with the two representative gel-based sample cleanup methods reported in literature, GGE-based strategy significantly improved the identification efficiency of proteins in terms of the number and coverage of the identified proteins.


Assuntos
Eletroforese em Gel de Gradiente Desnaturante/métodos , Proteínas de Membrana/análise , Mapeamento de Peptídeos/métodos , Proteoma/análise , Dodecilsulfato de Sódio/isolamento & purificação , Animais , Fígado/química , Fígado/citologia , Proteínas de Membrana/química , Proteínas de Membrana/classificação , Peso Molecular , Proteômica/métodos , Ratos , Dodecilsulfato de Sódio/química , Tripsina/química
19.
J Proteome Res ; 11(2): 818-28, 2012 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-22214374

RESUMO

We report an improved shotgun method for analyzing proteomic samples containing sodium dodecyl sulfate (SDS). This method is based on the use of strong-cation exchange (SCX) liquid chromatography (LC) for SDS removal that can be integrated with peptide separation as the first dimension of the two-dimensional LC tandem mass spectrometry workflow. To optimize the performance of SDS removal, various experimental conditions, including the concentrations of chemical reagents and salts in the sample, the SDS concentration, and the SCX mobile phase composition, were investigated. It was found that a peptide recovery rate of about 90% could be achieved while removing SDS efficiently. One key finding was that, by increasing the SDS concentration to a certain level (0.5%) in the digested peptide sample, the sample recovery rate could be increased. The peptide recovery rate of BSA digests was found to be 90.6 ± 1.0% (n = 3), and SDS in the SCX fractions collected was not detectable by pyrolysis GC-MS, i.e., below the detection limit of 0.00006% for the undesalted SCX fractions. The peptide recovery rates were found to be 90.9% ± 2.7 (n = 3) and 89.5% ± 0.5% (n = 3) for the digests of the membrane-protein-enriched fractions of E. coli cell lysates and the MCF-7 breast cancer cell line, respectively. Compared to the methods that use acid-labile surfactants, such as RapiGest and PPS, for the MCF-7 membrane fraction sample, the SDS method identified, on average (n = 3), more peptides (∼5%) and proteins (∼16%) than the RapiGest method, while the RapiGest method identified more peptides (∼21%) and proteins (∼7%) from the E. coli membrane fraction than the SDS method. In both cases, the two methods identified more peptides and proteins than the PPS method. Since SCX is widely used as the first dimension of 2D-LC MS/MS, integration of SDS removal with peptide separation in SCX does not add any extra steps to the sample handling process. We demonstrated the application of this method for 2D-LC MS/MS profiling of the MCF-7 membrane protein fraction and identified 6889 unique peptides, corresponding to 2258 unique proteins or protein groups from two replicate experiments with a false peptide discovery rate of ∼0.8%, compared to 5172 unique peptides and 1847 unique proteins identified by the RapiGest method.


Assuntos
Cromatografia por Troca Iônica/métodos , Fragmentos de Peptídeos/isolamento & purificação , Mapeamento de Peptídeos/métodos , Proteômica/métodos , Dodecilsulfato de Sódio/química , Cátions/química , Linhagem Celular Tumoral , Bases de Dados de Proteínas , Escherichia coli/química , Formiatos , Humanos , Limite de Detecção , Proteínas de Membrana/análise , Fragmentos de Peptídeos/análise , Dodecilsulfato de Sódio/isolamento & purificação , Tensoativos/química , Tensoativos/isolamento & purificação , Espectrometria de Massas em Tandem
20.
J Colloid Interface Sci ; 362(2): 524-31, 2011 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-21784429

RESUMO

In this work, the effect of SDS anionic surfactant on the diffusion-controlled evaporation rate of aqueous solution drops placed on TEFLON-FEP substrate was investigated with 11 different SDS concentrations. Drop evaporation was monitored in a closed chamber having a constant RH of 54-57% by a video camera. The initial contact angle, θ(i) decreased from 104±2° down to 68±1° due to the adsorption of SDS both at the water-air and the solid-water interfaces. The adsorption of SDS on the solid surface was found to be 76% of that of its adsorption at the water-air interface by applying Lucassen-Reynders approach. An equation was developed for the comparison of the evaporation rates of drops having different θ(i) on the same substrate. It was found that the addition of SDS did not alter the drop evaporation rate considerably for the first 1200 s for all the SDS concentrations. The main difference was found to be the change of the mode of drop evaporation by varying the SDS concentration. The constant θ mode was operative up to 80 mM SDS concentration, whereas constant contact area mode was operative after 200 mM SDS concentrations due to rapid drop pining on the substrate.


Assuntos
Dodecilsulfato de Sódio/isolamento & purificação , Volatilização , Adsorção , Difusão , Interações Hidrofóbicas e Hidrofílicas , Soluções , Água/química
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