Study Overview

Proteomics technologies are an integral part of biological and clinical research.  The ABRF Proteomics Standards Research Group (sPRG) functions to design and develop performance standards and resources for mass spectrometry-based proteomics applications. The sPRG is currently conducting a study based on the development of a new standard, derived from a series of isotopically-labeled peptides as internal standards, which may be useful for normalization in label-free and quantitative stable-isotope label-based analyses. We invite you to participate in a collaborative study that focuses on the ability of core facilities to determine relative quantitation of up to  1,000 heavy/light peptide pairs in a single sample, conserved across Homo sapiens, Mus musculus and Rattus norvegicus..

Goals

The primary goals of this study are the following:

• To allow labs to evaluate their ability to measure heavy/light peptide ratios for a large number of peptides both in an out of a complex biological background
• To give labs not familiar with heavy/light measurements and data analysis methods the opportunity to learn the technique
• To benchmark the standard across a large number of labs

Sample

Laboratories requesting samples will receive a single vial containing a lyophilized mixture of heavy synthetic peptides combined with a tryptic digest of HEK293 cells. The peptides and digests are present in sufficient quantities (5 ug digest and 375 fmol each heavy peptide) to permit at least three technical replicates. We have also provided Skyline Files containing various fragmentation specific spectral Libraries (HCD, IT, and QTOF) and a FASTA file containing all 1,000 peptides in one concatenated sequence. Participants are asked to analyze the sample in triplicate using the LC-MS instrument platform of their choice and report peak area ratios and coefficients of variation.   After analysis participants are asked to complete an on-line survey, upload skyline results to Panorama, and raw data to the sPRG (via study anonymizer).

Eligibility 

This year’s study is once again open to both ABRF members and non-members. However, the total number of samples is limited, and priority will be given to ABRF members. Non-members are encouraged to join the ABRF (for more information, go to http://www.abrf.org). Vendors/sponsors are welcome to participate. Each laboratory interested in participating should only request one sample per lab.

Timeline

The sPRG anticipates beginning distribution of the samples on August 12 2013 and requests the resulting data to be returned by October 11, 2013 so that sufficient time will be available to tabulate the results and present them at the 2014 ABRF Meeting (March 22-25; Albuquerque, NM).

Sample Request

Requests for samples must be submitted by e-mail to sPRG2013@gmail.com prior to close of business on Septemeber 30, 2013.  Please include the words “Sample request” in the subject line of the message and provide a contact name, affiliation, and complete mailing address in the body of the message. To reiterate, because of limited availability and the significant effort involved in preparation of the samples by the sPRG, the Research Group asks that samples only be requested if there is a reasonable probability that you will be able to return data by the deadline.  And as a bonus, each lab returning results will receive and additional aliquot of the sample for their own use. As in the past, result submissions will be coded to insure anonymity of the participating laboratories. A summary of the results of this study will be presented orally and as a poster at the ABRF 2014 meeting; the results will be subsequently posted on the ABRF website and will ultimately be published.

Study Sample Instructions

Instructions for completing the can be found in the pdf entitled "ABRF_sPRG_2013_Study_Sample_Instructions_FINAL.pdf" located at the bottom of this page

Survey and Data Results Submission

Study Participants need to complete the following:

  1. Report Peak Area Ratios using either an

      - Excel template (upload to sPRG 2013 FTP fileserver)

       or

      - Skyline and Panorama 

  2. Raw data upload

      Please upload your raw data to the sPRG 2013 FTP filesever

   3. Complete Study Survey

       http://www.surveymonkey.com/s/XLMP2WV

Thank you for participating in the Proteomics Standards Research Group 2013 study.

Sincerely,

 The ABRF Proteomics Standards Research Group:

Dr. Christopher Colangelo (Chair) - Yale University

Dr. Craig P. Dufresne - Thermo Fisher Scientific

Dr. David Hawke - UT MD Anderson Cancer Center

Dr. Alexander R. Ivanov - Northeastern University

Dr. Antonius Koller - Stony Brook University

Brendan MacLean - University of Washington 

Dr. Kristie L. Rose - Vanderbilt University Medical Center

Dr. Paul A Rudnick - NIST

Brian C. Searle - Proteome Software Inc.

Dr. Scott A. Shaffer - University of Massachusetts Medical School

Dr. Brett S Phinney (EB Liaison) - Proteomics Core UC Davis Genome Center

Sample

Laboratories requesting samples will receive a single vial containing a lyophilized mixture of heavy synthetic peptides combined with a tryptic digest of HEK293 cells. The peptides and digests are present in sufficient quantities (5 ug digest and 375 fmol each heavy peptide) to permit at least three technical replicates. We have also provided Skyline Files containing various fragmentation specific spectral Libraries (HCD, IT, and QTOF) and a FASTA file containing all 1,000 peptides in one concatenated sequence. Participants are asked to analyze the sample in triplicate using the LC-MS instrument platform of their choice and report peak area ratios and coefficients of variation.   After analysis participants are asked to complete an on-line survey, upload skyline results to Panorama, and raw data to the sPRG (via study anonymizer).

Eligibility 

This year’s study is once again open to both ABRF members and non-members. However, the total number of samples is limited, and priority will be given to ABRF members. Non-members are encouraged to join the ABRF (for more information, go to http://www.abrf.org). Vendors/sponsors are welcome to participate. Each laboratory interested in participating should only request one sample per lab.

Timeline

The sPRG anticipates beginning distribution of the samples on July 1, 2013 and requests the resulting data to be returned by September 1, 2013 so that sufficient time will be available to tabulate the results and present them at the 2014 ABRF Meeting (March 22-25; Albuquerque, NM).

Requests for samples must be submitted by e-mail to sPRG2013@gmail.com prior to close of business on September 30, 2013.  Please include the words “Sample request” in the subject line of the message and provide a contact name, affiliation, and complete mailing address in the body of the message. To reiterate, because of limited availability and the significant effort involved in preparation of the samples by the sPRG, the Research Group asks that samples only be requested if there is a reasonable probability that you will be able to return data by the deadline.  And as a bonus, each lab returning results will receive and additional aliquot of the sample for their own use. As in the past, result submissions will be coded to insure anonymity of the participating laboratories. A summary of the results of this study will be presented orally and as a poster at the ABRF 2014 meeting; the results will be subsequently posted on the ABRF website and will ultimately be published.

Study Participants need to complete the following:

1. Report Peak Area Ratios using either an

 -  Excel template (upload to sPRG 2013 FTP fileserver)

 or

 -  Skyline and Panorama 

2. Raw data upload

Please upload your raw data to the sPRG 2013 FTP filesever

3. Complete Study Survey

  http://www.surveymonkey.com/s/XLMP2WV

Mission:

Current Membership

Dr. Christopher Colangelo (Chair) - Yale University

Dr. Craig P. Dufresne - Thermo Fisher Scientific

Dr. David Hawke - UT MD Anderson Cancer Center

Dr. Alexander R. Ivanov - Northeastern University

Dr. Antonius Koller - Stony Brook University

Brendan MacLean - University of Washington 

Dr. Kristie L. Rose - Vanderbilt University Medical Center

Dr. Paul A Rudnick - NIST

Brian C. Searle - Proteome Software Inc.

Dr. Scott A. Shaffer - University of Massachusetts Medical School

Dr. Brett S Phinney (EB Liaison) - Proteomics Core UC Davis Genome Center