LC/MS/MS SPECTRA

The tandem mass spectra for 14 LC/MS/MS runs on control mixture A and 8 LC/MS/MS runs on control
mixture B are available to the public as .RAW and .dta files.  They can be downloaded from a password
protected web site to which you can gain access.

This work was supported by ISB and DOE Genomes to Life's grant to E. Kolker, now at  BIATECH. In
order to obtain these data, you need to email us first.

If you are working for nonprofit research/educational institutions, please send email to David Shteynberg
dshteynb@systemsbiology.org with the following text in the body of your email:
     "We would like to receive the data published in A.Keller et al, OMICS 6(2) 207-212 (2002). We will
     use the data for non-commercial purposes only.  We are full-time employees working in a nonprofit
     institution. While using these data, we will reference the above manuscript."

If you are working for profit organizations, please send email to Eugene Kolker ekolker@biatech.org
with your address,  phone, & fax.
 
 

CORRECT SEQUEST SEARCH RESULTS USING APPENDED HUMAN PEPTIDE SEQUENCE
DATABASE

Correct peptide assignments to spectra resulting from searching the human  peptide database (appended
with sequences of the 18 control mixture proteins and common sample contaminants)with SEQUEST.
Correct assignments were identified as those corresponding to the 18 control mixture proteins or identified
sample contaminants.  All such assignments assessed to be due to chance alone were removed from the list.
Spectra that were incorrectly assigned to peptides as a result of this analysis could be correctly assigned
using alternative analysis methods, or searching against a different sequence database.

Correct Peptide Assignments for:
           Spectra of Singly Charged Ions
           Spectra of Doubly Charged Ions
           Spectra of Triply Charged Ions
 

SUPPLEMENTAL IDENTIFICATION DATA

UCSD_supplemental_identifications.txt
Identifications contributed by http://www-cse.ucsd.edu/groups/bioinformatics/index.html. Tab-delimited text file of spectra annotated by InsPecT (Tanner, S., Shu, H., Frank, A., Wang, L.-C., E., Z., Mumby, M., Pevzner, P., and Bafna, V. InsPecT: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra. Anal. Chem. (in press), 2005.) with an annotation of p-value 0.05 or better from the 18-protein mixture data-set. These annotations refer to modified (mutated) peptides in the ISB dataset. (These spectra have not been manually validated, so the list may include some false positives.)