≡   PeptideAtlas Links Seattle Proteome Center

PeptideAtlas: Home Overview Contacts Publications Software Database Schema Feedback Funding FAQ
Atlas Data: Data Repository HPPP Data Central PeptideAtlas Builds PeptideAtlas Exports THISP Search Database
Contribute Data

Related: SRMAtlas PASSEL SWATHAtlas
Spectral Libs: Libraries + Info SpectraST Search

Glossary/Terms: Atlas nomenclature Protein ID terms

LOG IN
MENU
Log In
Search All Builds Select Build Stats & Lists Peps & Prots for Default Builds Summarize Peptide View Ortholog Group Current Build Peptide Protein Queries Browse Peptides Browse Proteins Browse Core Proteome Browse PTM Summary Browse Protein By Experiment Compare Proteins in 2 Builds Search Proteins Pathways HPP Protein Lists SRMAtlas Query Transitions Transition Lists SRMAtlas Builds PASSEL Experiments PASSEL Data Submission SWATH/DIA Download Library Custom Library Assess Library Upload Library

View Dataset

Email address      Password

Dataset Identifier
Metadata
datasetIdentifierPASS00011
datasetTypeSRM
submitterTerry Farrah <terry.farrah@systemsbiology.org>
submitter_organizationISB
lab_head_full_nameRuedi Aebersold
lab_head_emailaebersold@imsb.biol.ethz.ch
lab_head_organizationIMSB
lab_head_countrySwitzerland
datasetTagATAQS_cell_line
datasetTitleATAQS T-47D Cell Line
publicReleaseDate2011-11-13 00:00:00
finalizedDate2011-11-13 15:02:25
summaryThis set was prepared to target 50 peptides from 32 protein kinases in tryptic digests of extracts of the T-47D human ductal breast epithelial tumor cell line. The cell line was grown and lysed and the lysate was digested with trypsin. Fifty heavy-labeled reference peptides corresponding to PTP's of the targeted kinases were spiked into the total cell lysate. Sample sets containing 2 μg digested protein mass and 8, 40 and 200 fmol of each of the isotopically labeled reference peptides were measured in triplicate. The kinase protein list is also included in the ATAQS database. The project description was annotated in the ATAQS 'Project setup' and the protein list was populated in the 'Generate Protein List' step. We also investigated the candidate protein list in the context of protein networks using PIPE2 (Figure ​(Figure3).3). PIPE2 provides utilities to explore functionalities, cellular location and protein-protein interaction for the candidate kinase proteins and notes additional protein candidates which can be pursued in future studies, e.g. by targeting mass spectrometry. The PIPE2 analysis indicated that our selected candidate proteins are associated with known cancer genes (e.g., BRCA). Eight to ten transitions were selected and equal amounts of decoy transitions were added. A total of 1896 transitions were divided into four transition sets. A total of 36 LC-MS SRM experiments (3 dilutions times triplicate runs times 4 sets of transitions) were performed. Both datasets were measured using the ABSCIEX 4000 QTRAP mass spectrometer. Human protein kinases were targeted by SRM from total human cell lysate and the data were analyzed using the entire ATAQS workflow.
contributorsUlrike Kusebauch
publicationBrusniak M-Y K, Kwok S-T, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R, ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry, BMC Bioinformatics 12:78 pp1-15, 2011. PMID: 21414234
growth
treatment
extraction
separation
digestion
acquisition
informatics
instruments4000 Q-Trap
speciesHuman
massModificationsC+57.021464
Heavy isotope labelling on K & R
Official URL for this dataset: http://www.peptideatlas.org/PASS/PASS00011
To access files via FTP, use credentials:
Servername: ftp.peptideatlas.org
Username: PASS00011
Password: FI2457ye

Or use your browser's FTP mode: ftp://PASS00011:FI2457ye@ftp.peptideatlas.org/

Listing of files:

 3.7M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s1.mzXML
 3.3M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s10.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s10_scores.xls
 3.3M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s11.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s11_scores.xls
 2.9M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s12.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s12_scores.xls
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s1_scores.xls
 3.5M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s2.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s2_scores.xls
 3.6M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s3.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s3_scores.xls
 3.4M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s4.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s4_scores.xls
 3.4M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s5.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s5_scores.xls
 3.3M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s6.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s6_scores.xls
 3.4M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s7.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s7_scores.xls
 3.4M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s8.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s8_scores.xls
 3.3M Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s9.mzXML
    0 Nov 13  2011 4Q20100303uk_bgal_QC_ATAQS-s9_scores.xls
  46M Nov 13  2011 4Q20100303uk_set1a_ATAQS_200f_1-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_200f_1-s1_scores.xls
  45M Nov 13  2011 4Q20100303uk_set1a_ATAQS_200f_2-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_200f_2-s1_scores.xls
  45M Nov 13  2011 4Q20100303uk_set1a_ATAQS_200f_3-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_200f_3-s1_scores.xls
  46M Nov 13  2011 4Q20100303uk_set1a_ATAQS_40f_1-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_40f_1-s1_scores.xls
  45M Nov 13  2011 4Q20100303uk_set1a_ATAQS_40f_2-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_40f_2-s1_scores.xls
  44M Nov 13  2011 4Q20100303uk_set1a_ATAQS_40f_3-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_40f_3-s1_scores.xls
  48M Nov 13  2011 4Q20100303uk_set1a_ATAQS_8f_1-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_8f_1-s1_scores.xls
  47M Nov 13  2011 4Q20100303uk_set1a_ATAQS_8f_2-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_8f_2-s1_scores.xls
  46M Nov 13  2011 4Q20100303uk_set1a_ATAQS_8f_3-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1a_ATAQS_8f_3-s1_scores.xls
  41M Nov 13  2011 4Q20100303uk_set1b_ATAQS_200f_1-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_200f_1-s1_scores.xls
  39M Nov 13  2011 4Q20100303uk_set1b_ATAQS_200f_2-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_200f_2-s1_scores.xls
  37M Nov 13  2011 4Q20100303uk_set1b_ATAQS_200f_3-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_200f_3-s1_scores.xls
  41M Nov 13  2011 4Q20100303uk_set1b_ATAQS_40f_1-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_40f_1-s1_scores.xls
  39M Nov 13  2011 4Q20100303uk_set1b_ATAQS_40f_2-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_40f_2-s1_scores.xls
  37M Nov 13  2011 4Q20100303uk_set1b_ATAQS_40f_3-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_40f_3-s1_scores.xls
  41M Nov 13  2011 4Q20100303uk_set1b_ATAQS_8f_1-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_8f_1-s1_scores.xls
  40M Nov 13  2011 4Q20100303uk_set1b_ATAQS_8f_2-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_8f_2-s1_scores.xls
  39M Nov 13  2011 4Q20100303uk_set1b_ATAQS_8f_3-s1.mzXML
  16K Nov 13  2011 4Q20100303uk_set1b_ATAQS_8f_3-s1_scores.xls
  40M Nov 13  2011 4Q20100304uk_set2a_ATAQS_200f_1-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_200f_1-s1_scores.xls
  37M Nov 13  2011 4Q20100304uk_set2a_ATAQS_200f_2-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_200f_2-s1_scores.xls
  36M Nov 13  2011 4Q20100304uk_set2a_ATAQS_200f_3-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_200f_3-s1_scores.xls
  40M Nov 13  2011 4Q20100304uk_set2a_ATAQS_40f_1-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_40f_1-s1_scores.xls
  38M Nov 13  2011 4Q20100304uk_set2a_ATAQS_40f_2-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_40f_2-s1_scores.xls
  36M Nov 13  2011 4Q20100304uk_set2a_ATAQS_40f_3-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_40f_3-s1_scores.xls
  40M Nov 13  2011 4Q20100304uk_set2a_ATAQS_8f_1-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_8f_1-s1_scores.xls
  38M Nov 13  2011 4Q20100304uk_set2a_ATAQS_8f_2-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_8f_2-s1_scores.xls
  37M Nov 13  2011 4Q20100304uk_set2a_ATAQS_8f_3-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2a_ATAQS_8f_3-s1_scores.xls
  36M Nov 13  2011 4Q20100304uk_set2b_ATAQS_200f_1-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_200f_1-s1_scores.xls
  35M Nov 13  2011 4Q20100304uk_set2b_ATAQS_200f_2-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_200f_2-s1_scores.xls
  34M Nov 13  2011 4Q20100304uk_set2b_ATAQS_200f_3-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_200f_3-s1_scores.xls
  36M Nov 13  2011 4Q20100304uk_set2b_ATAQS_40f_1-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_40f_1-s1_scores.xls
  34M Nov 13  2011 4Q20100304uk_set2b_ATAQS_40f_2-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_40f_2-s1_scores.xls
  33M Nov 13  2011 4Q20100304uk_set2b_ATAQS_40f_3-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_40f_3-s1_scores.xls
  36M Nov 13  2011 4Q20100304uk_set2b_ATAQS_8f_1-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_8f_1-s1_scores.xls
  34M Nov 13  2011 4Q20100304uk_set2b_ATAQS_8f_2-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_8f_2-s1_scores.xls
  33M Nov 13  2011 4Q20100304uk_set2b_ATAQS_8f_3-s1.mzXML
  16K Nov 13  2011 4Q20100304uk_set2b_ATAQS_8f_3-s1_scores.xls
 2.4K Nov 13  2011 PASS00011_DESCRIPTION.txt
 165K Nov 13  2011 mbrusniak_Kinase_32_tlv_trans_input.csv
 3.6K Nov 13  2011 mbrusniak_Kinase_Transition_error.xls
  36K Nov 13  2011 mbrusniak_Kinase_Transition_top_pg.xls

Browse FTP upload area

PeptideAtlas
© 2004-2024 Institute for Systems Biology, All Rights Reserved