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Hs_Hela_LysC-Try_CID

ABSTRACT: Human hela proteome, Lysc and Trypsin CID

REANALYSIS of: PXD000900

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Others

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

PROVIDER: PAe004993 | PeptideAtlas | 2014-12-31

REPOSITORIES: PeptideAtlas

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Publications

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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Correction To - Confetti: A Multi-protease Map of the HeLa Proteome for Comprehensive Proteomics

Project description:Contains corrected HeLa SAX fractionated datasets for the Trypsin, LysC, and Chymotrypsin-Trypsin digests of the Confetti project. Original submission was PXD000900. Together with PXD000900 this submission makes up the dataset used for Confetti build 1.2.

2014-08-28 | PXD001258 | Pride

Broad spectrum antibodies to self-antigens and cytokines in RAG deficiency

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Hs_Hela_LysC_CID

Project description:Human hela proteome, LysC CID

2014-12-31 | PAe005063 | PeptideAtlas

Sensitivity and protein digestion course of proteomic Filter Aided Sample Preparation

Project description:1. Sensitivity of FASP was tested using SDS lysates from HeLa cells and mouse brain. Peptides were analyzed using a QExactive HF-X instrument. We found that FASP allows effective processing samples at the low and sub-microgram range. 2. Whole cell lysates of Hela cells were processed with FASP using single or double, consecutive or successive, digestion with LysC or trypsin. The generated peptides were analyzed using a LTQ-Orbitrap mass spectrometer. The results show that short digestion times apparently do not affect the number of identified proteins.

2019-11-12 | PXD014288 | Pride

Hs_Hela_Try_CID

Project description:Human hela proteome, Trypsin CID

2014-12-31 | PAe004984 | PeptideAtlas

Tandem LysC/trypsin digestion performs efficient in detergent conditions and under constant denaturating environments

Project description:All shotgun proteomics experiments rely on efficient proteolysis steps for sensitive peptide/protein identification and quantification. Continuous protocol improvement is therefore a constant topic in proteomics research. Previous reports suggest that the sequential tandem LysC/trypsin digest yields higher recovery of fully tryptic peptides than single-tryptic proteolysis. Based on the previous studies, it is assumed that the advantageous effect of tandem proteolysis requires a high sample denaturation state for the initial LysC digest. Therefore, to date, all systematic assessments of LysC/trypsin proteolysis were done in chaotropic environments such as urea. Here we show that the LysC/trypsin digestion can be carried with high efficiency in MS-compatible detergents resulting in higher yields of fully cleaved peptides. We show that higher cleavage efficiency of tandem digests has an impact on absolute protein quantification using iBAQ values. By additionally testing different urea tandem conditions our data implies that beneficial effects of the initial LysC digest do not depend on the sample denaturation state, but more likely, are due to different target specificities of LysC and trypsin. The observed detergent compatibility enables tandem digestion schemes to be implemented in efficient cellular solubilization proteomics procedures without the need for buffer exchange to chaotropic digestion environment.

2020-04-30 | PXD013273 | Pride

Hs_Hela_ArgC-LysC_CID

Project description:Human hela proteome, ArgC and LysC CID

2014-12-31 | PAe005034 | PeptideAtlas

Reanalysis of Pandey lab's draft of the human proteome

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

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