Blood plasma high abundant protein depletion unintentionally carries over 100 proteins

Silva-Costa, Lícia C.; Garcia-Rosa, Sheila; Smith, Bradley J.; Baldasso, Paulo A.; Steiner, Johann; Martins‐de‐Souza, Daniel

doi:10.1002/sscp.201900057

Cited by 8 publications

(4 citation statements)

References 32 publications

(44 reference statements)

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“…Proteins were transferred (2 h, 28 V) from the gel onto PVDF membrane (Hybond P, 0.2 μm) using two sheets of thick paper (Bio-Rad, Hercules, CA, USA), saturated with 48 mM Tris, 39 mM glycine, 0.037% SDS, 20% ethanol. The membrane was treated following a protocol of Blue Dry Western [ 36 ] and treated with antibodies [ 21 ]. Primary antibodies were mouse monoclonal anti-Hp (C8, sc-376893, or F8, sc-390962, from “Santa Cruz Biotechnology”, Santa Cruz, CA, USA) in dilution 1/25 (80 ng/mL in TBS (25 mM), Tris (pH 7.5) and 150 mM NaCl containing 3% ( w / v ) BSA) or rabbit polyclonal anti-Hp (MBS177476, MyBioSource, San Diego, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

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Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers

Naryzhny

Ronzhina

Zorina

et al. 2022

IJMS

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The use of tumor markers aids in the early detection of cancer recurrence and prognosis. There is a hope that they might also be useful in screening tests for the early detection of cancer. Here, the question of finding ideal tumor markers, which should be sensitive, specific, and reliable, is an acute issue. Human plasma is one of the most popular samples as it is commonly collected in the clinic and provides noninvasive, rapid analysis for any type of disease including cancer. Many efforts have been applied in searching for “ideal” tumor markers, digging very deep into plasma proteomes. The situation in this area can be improved in two ways—by attempting to find an ideal single tumor marker or by generating panels of different markers. In both cases, proteomics certainly plays a major role. There is a line of evidence that the most abundant, so-called “classical plasma proteins”, may be used to generate a tumor biomarker profile. To be comprehensive these profiles should have information not only about protein levels but also proteoform distribution for each protein. Initially, the profile of these proteins in norm should be generated. In our work, we collected bibliographic information about the connection of cancers with levels of “classical plasma proteins”. Additionally, we presented the proteoform profiles (2DE patterns) of these proteins in norm generated by two-dimensional electrophoresis with mass spectrometry and immunodetection. As a next step, similar profiles representing protein perturbations in plasma produced in the case of different cancers will be generated. Additionally, based on this information, different test systems can be developed.

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Section: Methodsmentioning

confidence: 99%

“…Nine proteins (IgG, apolipoprotein A1, apolipoprotein A2, transferrin, fibrinogen, haptoglobin, alpha1-antitrypsin, transthyretin) make up 40%, another 12 make up the next 9%, and the rest only 1%. Accordingly, it is common practice to remove the most abundant proteins (deplete) before deep proteomics analysis of plasma [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers

Naryzhny

Ronzhina

Zorina

et al. 2022

IJMS

View full text Add to dashboard Cite

show abstract

“…Proteins were transferred (2 h, 28 V) from the gel onto PVDF membrane (Hybond P, 0.2 μm) using two sheets of thick paper (Bio-Rad, USA), saturated with 48 mM Tris, 39 mM glycine, 0,037% SDS, 20% ethanol. The membrane was treated following a protocol of Blue Dry Western [36] and treated with antibodies [21]. Primary antibodies were mouse monoclonal anti-Hp (C8, sc-376893, or F8, sc-390962, from Santa Cruz Biotechnology, USA) in dilution 1/25 (80 ng/ml in TBS [25 mM Tris (pH 7.5) and 150 mM NaCl containing 3% [w/v] BSA) or rabbit polyclonal anti-Hp (MBS177476, MyBioSource, San Diego, CA, USA).…”

Section: Esi Lc-ms/ms Analysismentioning

confidence: 99%

Construction of 2DE-Patterns of Plasma Proteins: Aspect of Potential Tumor Markers

Naryzhny¹,

Ронжина²,

Zorina³

et al. 2022

Preprint

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Cancer is a complex systemic disease that changes the entire proteome. The analysis of this transformation makes it possible to determine tumor markers, that is, the most characteristic biomacromolecules produced by tumor cells. Here, the question of finding ideal tumor markers, which should be sensitive, specific, and reliable, is an acute issue. Unfortunately, none of the tumor markers, even those used in the clinic, has all these characteristics. Despite this, many tumor markers have demonstrated excellent clinical relevance for monitoring the effectiveness of different treatments for cancer patients. The use of markers also aids in the early detection of cancer recurrence and prognosis. Therefore, the situation in this area can be improved in two ways – by attempting to find an ideal single tumor marker or generating panels of different markers. In both cases, proteomics certainly plays a major role. Human plasma is one of the most popular samples as it is commonly collected in the clinic and provides noninvasive, rapid analysis for any type of disease including cancer. Many efforts have been applied in searching for “ideal” tumor markers digging very deep plasma proteome. There is a line of evidence that the most abundant, so-called “classical plasma proteins”, may be used to generate a tumor biomarker profile. To be comprehensive these profiles should have information not only about protein levels but proteoform distribution for each protein. Initially, the profile of these proteins in norm should be generated. Here, we present data about these profiles generated by two-dimensional electrophoresis with the following mass-spectrometry and immunodetection.

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“…Several techniques for the depletion of human blood plasma exist but immunoaffinity chromatography fractionation prior to mass spectrometry analysis represents the stateof-the-art in this matter, serving to increase the analytical power of sample analysis (GARCIA et al, 2017;JAROS et al, 2013c;SILVA-COSTA et al, 2019;TU et al, 2010). When high-performance liquid chromatography (LC) coupled online with mass spectrometry emerged, it gave rise to shotgun proteomics, a type of analysis where a mixture of digested proteins --peptides --are separated by reverse-phase chromatography (LINK et al, 1999a) before their mass is analyzed.…”

Section: Keymentioning

confidence: 99%

Compreensão da depressão geriátrica através da biologia de sistemas a partir da análise proteômica de plasma sanguíneo

Corrêa¹

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Dedico este trabalho a minha mãe, Elisete, meu pai, Jurandir, e ao meu padrasto, Alex, que me deram suporte incondicional quando, a certa altura da vida, decidi mudar tudo que tinha feito até então, para me aventurar como cientista. Foi por causa da fé que eles tinham em mim que reuni coragem pra seguir o que fazia meus olhos brilharem e meu coração bater mais forte."Somewhere, something incredible is waiting to be known." -Carl Sagan "Let us think the unthinkable, let us do the undoable, let us prepare to grapple with the ineffable itself, and see if we may not eff it after all." -Douglas Adams AGRADECIMENTOSO presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Brasil (CAPES) -Código de Financiamento 001.Agradeço o apoio da Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), processo nº 2018/03422-7.Minha profunda gratidão à minha família, que me encorajou e apoiou até aqui. Agradeço também ao meu orientador, Prof. Daniel Martins-de-Souza, por acreditar no meu trabalho, e por oferecer inúmeras oportunidades de crescimento.Agradeço aos meus amigos do LNP, em especial Aline, a maior cientista que conheço, pelo companheirismo, discussões sobre ciência, músicas de tema de novela dos anos 90 e noites de jogos de tabuleiro. Falando em jogos de tabuleiro, Ana Carol, Brad, Pam, Lívia, Verônica, JuMi, obrigada por tornarem o ambiente de trabalho -e fora dele -tão gostoso. Brad, obrigada por me ajudar a escrever melhor em inglês, e por todas as correções que você já fez pra gente. Obrigada ao Victor Corasolla, vulgo Vitinho, por suas dicas e disposição infinita em ajudar todo mundo. Agradeço ao Prof. Breno Diniz, pela coorientação em todos os momentos deste trabalho, mas em especial logo depois da minha qualificação, quando mais precisei que alguém me encorajasse. Ao prof. Benilton de Carvalho, obrigada por me orientar com a estatística. Ao Gustavo Souza, obrigada por compartilhar um pouco da sua imensa experiência em MS comigo.Ainda, sou grata às pessoas que me cercaram, neste período, me oferecendo ouvidos, comida, café ou cerveja e, em todos os casos, amizade. Carol Marcondes, obrigada por me ensinar a ficar pistola: isso ainda vai salvar minha vida.Dani Baldner, Bete, Eliane, Rosi Barcelos, Thiago, Virgínia e Valdir, obrigada por me oferecerem um porto seguro.Agradeço também aos meus atuais 7 gatos (Lion, Sofia, Tony, Selina, Madalena, Arnesto e Álvaro) e meu cachorro idosinho Fred, pela companhia nessa aventura. Vocês não sabem e nem se importam com o que isso significa, desde que eu traga petiscos, mas sem vocês meu coração não estaria inteiro. RESUMOO distúrbio chamado depressão geriátrica, ou, em inglês, late-life depression (LLD) corresponde a episódios depressivos que ocorrem por volta dos 60 anos de idade ou mais, mas possui mecanismos fisiopatológicos do LLD distintos da depressão maior. Assim, uma visão integrada dos processos biológicos e das vias bioquímicas alteradas em pacientes com LLD pode contribuir para o diagnóstico, acompanhamento da r...

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Blood plasma high abundant protein depletion unintentionally carries over 100 proteins

Cited by 8 publications

References 32 publications

Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers

Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers

Construction of 2DE-Patterns of Plasma Proteins: Aspect of Potential Tumor Markers

Compreensão da depressão geriátrica através da biologia de sistemas a partir da análise proteômica de plasma sanguíneo

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