Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

Carvalho, Paulo C.; Lima, Diogo Borges; Leprevost, Felipe V.; Santos, Marlon D.M.; Fischer, Juliana de Saldanha da Gama; Aquino, Priscila Ferreira de; Moresco, James J.; Yates, John R.; Barbosa, Valmir C.

doi:10.1038/nprot.2015.133

Cited by 217 publications

(167 citation statements)

References 66 publications

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“…PatternLab’s isobaric analyzer module was employed for pinpointing differentially abundant proteins when comparing the profound tissue samples from the first and second surgery as described in our bioinformatics protocol (16). PatternLab’s Gene Ontology Explorer module (20) and (21) were used to help interpret the data.…”

Section: Methodsmentioning

confidence: 99%

A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme

Aquino¹,

Carvalho

Nogueira

et al. 2016

Front. Oncol.

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Tumors consist of cells in different stages of transformation with molecular and cellular heterogeneity. By far, heterogeneity is the hallmark of glioblastoma multiforme (GBM), the most malignant and aggressive type of glioma. Most proteomic studies aim in comparing tumors from different patients, but here we dive into exploring the intratumoral proteome diversity of a single GBM. For this, we profiled tumor fragments from the profound region of the same patient’s GBM but obtained from two surgeries a year’s time apart. Our analysis also included GBM‘s fragments from different anatomical regions. Our quantitative proteomic strategy employed 4-plex iTRAQ peptide labeling followed by a four-step strong cation chromatographic separation; each fraction was then analyzed by reversed-phase nano-chromatography coupled on-line with an Orbitrap-Velos mass spectrometer. Unsupervised clustering grouped the proteomic profiles into four major distinct groups and showed that most changes were related to the tumor’s anatomical region. Nevertheless, we report differentially abundant proteins from GBM’s fragments of the same region but obtained 1 year apart. We discuss several key proteins (e.g., S100A9) and enriched pathways linked with GBM such as the Ras pathway, RHO GTPases activate PKNs, and those related to apoptosis, to name a few. As far as we know, this is the only report that compares GBM fragments proteomic profiles from the same patient. Ultimately, our results fuel the forefront of scientific discussion on the importance in exploring the richness of subproteomes within a single tissue sample for a better understanding of the disease, as each tumor is unique.

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Section: Methodsmentioning

confidence: 99%

A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme

Aquino¹,

Carvalho

Nogueira

et al. 2016

Front. Oncol.

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“…15 Briefly, identifications were grouped by charge state (+2 and ≥ +3) and then by tryptic status (fully tryptic, semitryptic), resulting in four distinct subgroups. 13 The advantage of NIAF is that its normalization process accounts for the protein size, thus penalizing proteins with more theoretical peptides. The identifications were sorted in nondecreasing order according to the discriminator score.…”

Section: Mass Spectra Data and Bioinformatics Analysismentioning

confidence: 99%

Interactome analysis of the human Cap‐specific mRNA (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1) protein

Simabuco

Pavan

Pestana

et al. 2018

J of Cellular Biochemistry

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In a previous study, we have shown that the gene promoter of a protein termed KIAA0082 is regulated by interferon and that this protein interacts with the RNA polymerase II. It has been subsequently shown that KIAA0082 is the human cap‐specific messenger RNA (mRNA) (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1), which catalyzes methylation of the 2′‐O ‐ribose of the first nucleotide of capped mRNAs. Pre‐mRNAs are cotranscriptionally processed, requiring coordinate interactions or dissociations of hundreds of proteins. hMTr1 potentially binds to the 5′‐end of the whole cellular pre‐mRNA pool. Besides, it contains a WW protein interaction domain and thus is expected to be associated with several proteins. In this current study, we determined the composition of complexes isolated by hMTr1 immunoprecipitation from HEK293 cellular extracts. Consistently, a large set of proteins that function in pre‐mRNA maturation was identified, including splicing factors, spliceosome‐associated proteins, RNA helicases, heterogeneous nuclear ribonucleoproteins (HNRNPs), RNA‐binding proteins and proteins involved in mRNA 5′‐ and 3′‐end processing, forming an extensive interaction network. In total, 137 proteins were identified in two independent experiments, and some of them were validated by immunoblotting and immunofluorescence. Besides, we further characterized the nature of several hMTr1 interactions, showing that some are RNA dependent, including PARP1, ILF2, XRCC6, eIF2α, and NCL, and others are RNA independent, including FXR1, NPM1, PPM1B, and PRMT5. The data presented here are consistent with the important role played by hMTr1 in pre‐mRNA synthesis.

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“…The peptides were subjected to LC-MS/MS analysis using a Thermo Scientific Easy-nLC 1000 ultra- The Comet 2015 rev. 2 search engine [24], which is embedded into PatternLab for proteomics 4.0 [25], was used to compare experimental tandem mass spectra against those theoretically generated from our sequence database and select the most likely peptide sequence candidate for each spectrum. Briefly, the search was limited to fully peptide candidates; we imposed carbamidomethylation of cysteine and oxidation of methionine as fixed and variable modification, respectively.…”

Section: Lc-ms/ms Acquisitionmentioning

confidence: 99%

Identification of potential targets for an anticoagulant pectin

Santana¹,

Gracher²,

Rüdiger³

et al. 2017

Journal of Proteomics

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Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

Cited by 217 publications

References 66 publications

A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme

A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme

Interactome analysis of the human Cap‐specific mRNA (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1) protein

Identification of potential targets for an anticoagulant pectin

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