====== 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) [[https://cptac-data-portal.georgetown.edu/cptacPublic|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.

The libraries were updated on March 16, 2022 to make them compatible with Proteome Discoverer. Previous versions are available on request.

<WRAP center group 90%>
^ 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| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best.msp.tar.gz|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 [[peptidew:mspepsearch|MS Search or MSPepSearch]] and by the MSPepSearch node within Proteome Discoverer. |  4.9GB \\ 649MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best_1.tar.gz|Download1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best_2.tar.gz|Download2]]  | 
| **cptac3_tmt_selected_passed_best.fasta.tar.gz** - FASTA file used to search CompRef human-mouse xenograft samples.|  13MB|[[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best.fasta.tar.gz|Download]]|
| **md5_checklist.chk** - MD5 hash file. |  1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/md5_checklist.chk|Download]] |
 
</WRAP>

  * 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.


<WRAP center group 90%>
^ 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| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best_decoy.msp.tar.gz|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 [[peptidew:mspepsearch|MS Search or MSPepSearch]] and by the MSPepSearch node within Proteome Discoverer. |  4.9GB \\ 642MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best_decoy_1.tar.gz|Download1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best_decoy_2.tar.gz|Download2]]  | 
| **md5_checklist.chk** - MD5 hash file. |  1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/md5_checklist.chk|Download]] |
 
</WRAP>



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