A three-pronged 'Pitchfork' strategy enables an extensive description of the human membrane proteome and the identification of missing proteins

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F19%3A00517774" target="_blank" >RIV/61388971:_____/19:00517774 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11110/19:10397761 RIV/00216208:11310/19:10397761

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S1874391919301836?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S1874391919301836?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jprot.2019.103411" target="_blank" >10.1016/j.jprot.2019.103411</a>

Result language

angličtina

Original language name

A three-pronged 'Pitchfork' strategy enables an extensive description of the human membrane proteome and the identification of missing proteins

Original language description

Integral membrane proteins are under-represented in standard proteomic analyses, mostly because of their low expression and absence of trypsin-cleavage sites in their hydrophobic transmembrane segments. Novel and effective strategies for membrane proteomic analysis aim at soluble N-glycosylated segments of integral membrane proteins (CSC, SPEG, N-glyco-FASP) or selectively target the hydrophobic transmembrane alpha-helical segments employing chemical peptide cleavage by CNBr (hpTC). We combined a solid phase enrichment of glycopeptides (SPEG) with a transmembrane segment-oriented hpTC method and a standard 'detergent and trypsin' approach into a three-pronged 'Pitchfork' strategy to maximize the membrane proteome coverage in human lymphoma cells. This strategy enabled the identification of > 1200 integral membrane proteins from all cellular compartments, including 105 CD antigens, 24 G protein-coupled receptors, and 141 solute carrier transporters. The advantage of the combination lies in the complementarity of the methods. SPEG and hpTC target different sets of membrane proteins. HpTC provided identifications of proteins and peptides with significantly higher hydrophobicity compared to SPEG and detergent-trypsin approaches. Among all identified proteins, we observed 32 so-called 'missing proteins'. The Pitchfork strategy presented here is universally applicable and enables deep and fast description of membrane proteomes in only 3 LC-MS/MS runs per replicate. Significance: Integral membrane proteins (IMPs) are encoded by roughly a quarter of human coding genes. Their functions and their specific localization makes IMPs highly attractive drug targets. In fact, roughly half of the currently approved drugs in medicine target IMPs. Our knowledge of membrane proteomes is, however, limited. We present a new strategy for the membrane proteome analysis that combines three complementary methods targeting different features of IMPs.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Proteomics

ISSN

1874-3919

e-ISSN

—

Volume of the periodical

204

Issue of the periodical within the volume

JUL 30

Country of publishing house

NL - THE KINGDOM OF THE NETHERLANDS

Number of pages

10

Pages from-to

103411

UT code for WoS article

000475994800013

EID of the result in the Scopus database

2-s2.0-85067021763