====== Human HCD iTRAQ Library  ======
=====  Peptide Library (Nov. 26, 2014) =====

The human HCD iTRAQ library was created entirely from raw data stored on the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data portal[[https://cptac-data-portal.georgetown.edu/cptacPublic/]].  Contributing laboratories were the Broad Institute, Johns Hopkins University and Pacific Northwest National Laboratory.

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^File - Description ^Size ^Link |
| **cptac2_human_hcd_itraq_selected_part1.msp.tar.gz** \\  **cptac2_human_hcd_itraq_selected_part2.msp.tar.gz**  \\ \\ Library divided into two parts due to memory limitations of some software. 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.  |  1.9GB \\ 2.0GB|  [[https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_selected_part1.msp.tar.gz|Download1]]  \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_selected_part2.msp.tar.gz|Download2]]  |
|**cptac2_human_hcd_itraq_selected_part1.tar.gz** \\ **cptac2_human_hcd_itraq_selected_part2.tar.gz** \\ \\ Consensus library in NIST binary format (two parts. The folders generated by extracting these packages can be used directly by [[:peptidew:mspepsearch|MS Search or MSPepSearch]] and by the MSPepsearch node within Proteome Discoverer. |  3.3GB \\ 3.6GB |  [[https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_selected_part1.tar.gz|Download1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_selected_part2.tar.gz|Download2]]|
| **20111201-RefSeq-Human-37-Mouse-37-Trypsin.fasta.tar.gz** - FASTA file used to search CompRef human-mouse xenograft samples.|16.2MB|[[https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/20111201_RefSeq_Human_37-Mouse_37_Trypsin.fasta.tar.gz|Download]]|
| **md5_checklist.chk** - MD5 hash file. |  1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/md5_checklist.chk|Download]] | 

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    * Total number of Spectra: **1,201,632**
    * Unique Peptide Sequences: **390,009**
    * Total Proteins in FASTA file used: **32,800**

=====  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.


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^File - Description ^Size ^Link |
| **cptac2_human_hcd_itraq_selected_part1_decoy.msp.tar.gz** \\  **cptac2_human_hcd_itraq_selected_part2_decoy.msp.tar.gz**  \\ \\ Library divided into two parts due to memory limitations of some software. 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, like Skyline, after unzipping.   |  1.9GB \\ 2.0GB|  [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy\Orbitrap-HCD_iTRAQ-4/cptac2_human_hcd_itraq_selected_part1_decoy.msp.tar.gz|Download1]]  \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_iTRAQ-4/cptac2_human_hcd_itraq_selected_part2_decoy.msp.tar.gz|Download2]]  |
|**cptac2_human_hcd_itraq_selected_part1_decoy.tar.gz** \\ **cptac2_human_hcd_itraq_selected_part2_decoy.tar.gz** \\ \\ Library of decoy spectra in NIST binary format (two parts). The folders generated by extracting these packages can be used directly by [[:peptidew:mspepsearch|MS Search or MSPepSearch]] and by the MSPepsearch node within Proteome Discoverer. |  3.7GB \\ 4.0GB |  [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_iTRAQ-4/cptac2_human_hcd_itraq_selected_part1_decoy.tar.gz|Download1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_iTRAQ-4/cptac2_human_hcd_itraq_selected_part2_decoy.tar.gz|Download2]]|
| **md5_checklist.chk** - MD5 hash file. |  1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_iTRAQ-4/md5_checklist.chk|Download]] | 

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