Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reanalysis dataset of JPST000207

ABSTRACT: Quantitative phosphoproteome analyses of colorectal cancer cell lines (metastatis: SW620, non-metastatis: SW480) were carried out using IMAC-based posphopeptide enrichment followed by SCX-RP-MS/MS with SILAC labeling (SW480: light-label, SW620: heavy-label). For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yasushi Ishihama

PROVIDER: RPXD018480 | JPOST Repository | Wed May 27 00:00:00 BST 2020

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	111229_pHL01.raw	Raw
	120105_pLH09.raw	Raw
	120105_pLH10.raw	Raw
	120105_pLH11.raw	Raw
	120105_pLH12.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Reanalysis dataset of JPST000208

Project description:Quantitative proteome analyses of colorectal cancer cell lines (metastatis: SW620, non-metastatis: SW480) were carried out using SCX-RP-MS/MS with SILAC labeling(SW480: light-label, SW620: heavy-label). For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-27 | RPXD018481 | JPOST Repository

Reanalysis dataset of JPST000203

Project description:Quantitative proteome analyses of colorectal cancer tissues from 24 patients (12 with or without metastasis) were carried out using SCX-RP-MS/MS with iTRAQ labeling(metastasis:iTRAQ115 or 117, no metastasis: iTRAQ114 or 116). For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-27 | RPXD018476 | JPOST Repository

Reanalysis dataset of JPST000210

Project description:Phosphoproteome analyses of colorectal cancer tissues from 20 patients (20 tumors and 20 tumor-adjacent normal tissues) were carried out using IMAC-based posphopeptide enrichment followed by SCX-RP-MS/MS. For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-27 | RPXD018482 | JPOST Repository

Reanalysis dataset of JPST000206

Project description:Quantitative phosphoproteome analyses of colorectal cancer cell lines (HCT116 metastatic clone and the parent clone without metastasis) were carried out using IMAC-based posphopeptide enrichment followed by SCX-RP-MS/MS with iTRAQ labeling(metastasis:iTRAQ116 or 117, no metastasis: iTRAQ114 or 115). For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-27 | RPXD018479 | JPOST Repository

Reanalysis dataset of JPST000204

Project description:Quantitative phosphoproteome analyses of colorectal cancer tissues from 24 patients (12 with or without metastasis) were carried out using IMAC-based posphopeptide enrichment followed by SCX-RP-MS/MS with iTRAQ labeling(metastasis:iTRAQ115 or 117, no metastasis: iTRAQ114 or 116). For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-27 | RPXD018477 | JPOST Repository

Reanalysis dataset of JPST000205

Project description:Quantitative proteome analyses of colorectal cancer cell lines (HCT116 metastatic clone and the parent clone without metastasis) were carried out using SCX-RP-MS/MS with iTRAQ labeling(metastasis:iTRAQ116 or 117, no metastasis: iTRAQ114 or 115). For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-27 | RPXD018478 | JPOST Repository

Reanalysis dataset of JPST000201

Project description:Human breast cancer tissue samples from 18 patients with high-risk or low-risk MammaPrint breast cancer were analyzed. The membrane fractions were enriched, and the extracted proteins were reduced, alkylated, digested with Lys-C and Trypsin, and labelled with iTRAQ4plex: 114; high risk; 115; low risk. For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.

2020-05-26 | RPXD018475 | JPOST Repository

WGBS analysis of various colon cancer cell lines

Project description:We profiled genome-wide DNA methylation in four cancer cell line, ie SW480-lenti SW480-TET2CD, SW620--lenti and SW620-TET2CD.

2020-07-21 | GSE154734 | GEO

RNA-seq analysis of various colon cancer cell lines treated with TGFb1 and repsox

Project description:Four cancer cell line, ie SW480-Vector, SW480-TET2, SW620-Vector and SW620-TET2 were treated with tgfb1, repsox and control. Then the total RNA of these samples were extracted and sequenced with Illumina Nextseq 500.

2020-07-18 | GSE154646 | GEO

MicroRNA expression profile between human colorectal cancer SW480 and SW620 cell line

Project description:Two isogenic human colorectal cancer cell lines (primary SW480 cell line and its lymph node metastatic variant SW620 cell line),as an in vitro metastatic model. We have demonstrated that SW620 cell line possesses high metastasis potential and SW480 cell linepossesses low metastatic potential.

2016-08-01 | GSE72412 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data