peptidew:lib:human_hcd_tmt

Human HCD TMT Library

Peptide Library (Oct. 30, 2019)

The human HCD TMT library was created entirely from raw data stored on the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data portal. Contributing laboratories were the Broad Institute, Johns Hopkins University and Pacific Northwest National Laboratory.

Unlike the previous CPTAC iTRAQ library, which contains spectra over a range of collisional energy, this TMT library contains a single spectrum for each peptide ion, selected based on score and its number of a, b, and y ion assignments.

File - Description Size Link
cptac3_tmt_selected_passed_best.msp.tar.gz
Consensus library in plain ASCII text (msp format). This format can be used as an exchange format. It is also directly readable by some software applications, including Skyline, after unzipping.
2.6GB Download
cptac3_tmt_selected_passed_best_part1.tar.gz
cptac3_tmt_selected_passed_best_part2.tar.gz
Consensus library in NIST binary format. The folder generated by extracting this package can be used directly by MS Search or MSPepSearch and by the MSPepSearch node within Proteome Discoverer.
4.8GB
654MB
Download1
Download2
cptac3_tmt_selected_passed_best.fasta.tar.gz - FASTA file used to search CompRef human-mouse xenograft samples. 13MBDownload
md5_checklist.chk - MD5 hash file. 1KB Download
  • Total number of Spectra: 597,548
  • Unique Peptide Sequences: 386,224
  • Total Proteins in FASTA file used: 37,742
  • Proteome Sequence Coverage: 29.09%

Decoy Library (Feb. 21, 2020)

The decoy library (sequence reversed) was created based on the methods described in the paper:
Zhang, Zheng, et al. “Reverse and random decoy methods for false discovery rate estimation in high mass accuracy peptide spectral library searches.” Journal of Proteome Research 17.2 (2018): 846-857.

File - Description Size Link
cptac3_tmt_selected_passed_best_decoy.msp.tar.gz
Library of decoy spectra in plain ASCII text (msp format). This format can be used as an exchange format. It is also directly readable by some software applications, including Skyline, after unzipping.
2.6GB Download
cptac3_tmt_selected_passed_best_decoy_1.tar.gz
cptac3_tmt_selected_passed_best_decoy_2.tar.gz
Library of decoy spectra in NIST binary format. The folder generated by extracting this package can be used directly by MS Search or MSPepSearch and by the MSPepSearch node within Proteome Discoverer.
4.9GB
642MB
Download1
Download2
md5_checklist.chk - MD5 hash file. 1KB Download

© Copyright information
These mass spectral libraries are protected by copyright law and may not be re-distributed without a valid Distribution Agreement. To receive such an agreement, contact the Standard Reference Data Program at the National Institute of Standards and Technology by emailing data@nist.gov or calling 301-975-2008.

peptidew/lib/human_hcd_tmt.txt · Last modified: 2020/02/25 15:10 (external edit)

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