PXD000269 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Minimalistic sample processing |
Description | Proteomic sample preparation typically involves multi-step workflows that can potentially perturb the biological system under analysis. These datasets were used to demonstrate that the entire processing pipeline, from cell lysis through elution of purified peptides, can be performed in a single, enclosed volume. This in-StageTip sample preparation method largely eliminates contamination or losses and is extremely robust and scalable. Peptides can be eluted in several fractions or in one step for single-run proteomics. In one day of gradient time we obtained the largest proteomes for budding and fission yeast to date. Applying the in-StageTip method to quadruplicate measurements of a human cell line yielded copy number estimates for more than 9000 human proteins. Data Analysis: MS raw files were analyzed by MaxQuant software (version 1.3.10.12) and peak lists were searched either against the human Uniprot FASTA database version 2/25/2012 (81213 entries), against the S. cerevisiae Uniprot FASTA database version 2/25/2012 (6649 entries) or the SGD based S. cerevisiae Fasta database orf_trans.20100105 (5904 entries), or against the S. pombe Uniprot FASTA database version 4/2/2013 (5096 entries) or pompep FASTA database version 4/2/2013 (5031 entries) and a common contaminants database (247 entries) by Andromeda search engine with cysteine carbamidomethylation as a fixed modification and N-terminal acetylation and methionine oxidation as variable modifications. False discovery rate (FDR) was set to 0.01 for proteins and peptides (minimum length of 7 amino acids) and was determined by searching a reverse database. Enzyme specificity was set as C-terminal to Arg and Lys, and a maximum of 2 miscleavages allowed. Peptide identification was performed with an allowed initial precursor mass deviation up to 7 ppm and an allowed fragment mass deviation 20 ppm. Quantification of SILAC pairs was carried out by MaxQuant with standard settings and without the re-quantification option. |
HostingRepository | PRIDE |
AnnounceDate | 2014-07-25 |
AnnouncementXML | Submission_2014-07-25_01:12:54.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Mario Oroshi |
SpeciesList | scientific name: Schizosaccharomyces pombe (Fission yeast); NCBI TaxID: 4896; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2013-05-28 15:42:05 | ID requested | |
1 | 2014-01-31 11:49:34 | announced | |
⏵ 2 | 2014-07-25 01:12:55 | announced | Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Yeast, in-depth proteome, human, copy number |
Contact List
Mario Oroshi |
contact affiliation | Proteomics |
contact email | oroshi@biochem.mpg.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000269
- Label: PRIDE project
- Name: Minimalistic sample processing