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Hs_Hela_ArgC-LysC_HCD

ABSTRACT: Human hela proteome, ArgC and LysC HCD

REANALYSIS of: PXD000900

INSTRUMENT(S): QExactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Others

SUBMITTER: Guo X, Trudgian DC, Lemoff A, Yadavalli S, Mirzaei H

PROVIDER: PAe005058 | PeptideAtlas | 2014-12-31

REPOSITORIES: PeptideAtlas

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Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics.

Guo Xiaofeng X Trudgian David C DC Lemoff Andrew A Yadavalli Sivaramakrishna S Mirzaei Hamid H

Molecular & cellular proteomics : MCP 20140402 6

Bottom-up proteomics largely relies on tryptic peptides for protein identification and quantification. Tryptic digestion often provides limited coverage of protein sequence because of issues such as peptide length, ionization efficiency, and post-translational modification colocalization. Unfortunately, a region of interest in a protein, for example, because of proximity to an active site or the presence of important post-translational modifications, may not be covered by tryptic peptides. Detec ...[more]

PMID: 24696503

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Hs_Hela_ArgC_HCD

Project description:Human hela proteome, ArgC HCD

2014-12-31 | PAe005046 | PeptideAtlas

Hs_Hela_LysC_HCD

Project description:Human hela proteome, LysC HCD

2014-12-31 | PAe005072 | PeptideAtlas

Verification of immunogenic nature by microarray screening

Project description:Screening of 22 novel proteins derived from Campylobacter jejuni NCTC 11168 identified prior via screening of cDNA libraries. The full-length proteins were attached using a specific HaloTag to their corresponding ligand surface, HaloLink. Screening was performed using three different polyclonal antibodies to Campylobacter jejuni and detection was achieved by goat polyclonal antibody to rabbit IgG conjugated with Chromeo-546. In order to assess their potential immungenic nature and rank the proteins investigated, comparative analysis using already described antigens from C. jejuni were used in the assay. Each microarray was separated into different incubation chambers using the ProPlate (Grace Biolabs) multi-well gaskets. While for two slides (2009 and 2447), three chambers were used, the remaining slides were designed to use 16 different compartments. Each compartment could be incubated with different antibodies and represent individual replicates of the slides. As positive references, hisJ and cjaA were used. For negative controls, argC and gapA were used, and the crude lysates of the expression host (Acella E. coli) and buffer were spotted as well. For slides 2009 and 2447, three-well gaskets were used allowing for seven replicates per sample, while only incubation with one antibody. Slides 416033 and 416826 used 16-well gaskets and only hisJ and argC as protein references. Samples and controls were spotted in quadruplicate. Finally, for 1000 and 1001, samples were spotted in triplicate, whereas controls were spotted in quadruplicate using hisJ, cjaA, argC and gapA as protein references.

2013-04-06 | E-GEOD-45520 | biostudies-arrayexpress

Quantifying missing (phospho)proteome regions with the broad-specificity protease subtilisin

Project description:Despite huge efforts to map the human proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%. Reasons for missing areas of the proteome comprise protease-resistant domains including the lack/excess of enzymatic cleavage sites, non-unique peptide sequences, impaired peptide ionization/separation and low expression levels. To access novel areas of the proteome the beneficial use of enzymes complementary to trypsin, such as GluC, AspN, LysN, ArgC, LysArginase has been reported. Here, we present how the broad-specificity protease subtilisin enables mapping of previously hidden areas of the proteome. We systematically evaluated its digestion efficiency and reproducibility and compared it to the gold standard in the field, trypsin. Notably, subtilisin allows reproducible near-complete digestion of cells lysates in 1 minute. As expected from its broad specificity the generation of overlapping peptide sequences reduces the number of identified proteins compared to trypsin (8,363 vs. 6,807; 1% protein FDR). However, subtilisin considerably improved the coverage of missing and particularly proline-rich areas of the proteome. Along 14,628 high confidence phosphorylation sites identified in total, only 33% were shared between both enzymes, while 37% were exclusive to subtilisin. Notably, 926 of these were not even accessible by additional in silico digestion with either AspN, ArgC, GluC, LysC, or LysN. Thus, subtilisin might be particularly beneficial for system-wide profiling of post-translational modification sites. Finally, we demonstrate that subtilisin can be used for reporter-ion based in-depth quantification, providing a precision comparable to trypsin – despite broad specificity and fast digestion that may increase technical variance.

2017-11-30 | PXD008068 | Pride

Hs_Hela_ArgC-LysC_CID

Project description:Human hela proteome, ArgC and LysC CID

2014-12-31 | PAe005034 | PeptideAtlas

Screening for novel immunogenic proteins of Campylobacter jejuni NCTC 11168

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2013-04-06 | GSE45268 | GEO

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2013-10-01 | GSE49605 | GEO

Reanalysis of Pandey lab's draft of the human proteome

Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.

2015-03-10 | E-PROT-1 | biostudies-arrayexpress

Profiling proteome-scale antibody responses to M. tuberculosis proteins in sera of macaques infected with M. tuberculosis

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