====== Consensus Human HCD Libraries ======
===== Peptide Libraries (May 19, 2020) =====
The consensus human HCD libraries were created using more than 10,000 raw files
* available on ProteomeXchange - http://www.proteomexchange.org
* generated at the Mass Spectrometry Data Center of the National Institute of Standards and Technology (NIST).
The libraries in the msp and NIST binary formats were updated on May 19, 2020. The new libraries of consensus spectra contain 86% more peptides than the previous version with 4-15% increase in the number of positive IDs returned for typical samples at FDR=0.01. Previous versions are available on request.
Methods used for building the libraries are presented at the ASMS 2020 conference: \\
**Filtering and optimization of peptide tandem mass spectral libraries.** \\
Authors: Sergey L. Sheetlin, Guanghui Wang, Dmitrii V. Tchekhovskoi , Zheng Zhang, Stephen E. Stein \\
The poster is available for {{:peptidew:sergey_sheetlin_asms2020.pdf| download }}. \\
The meaning of the fields present in the comments of the library spectra can be found {{:peptidew:description_of_comment_fields.pdf| here }}. \\
^ File - Description ^ Size ^ Link ^
^ //Libraries of selected 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:// ^
| Library 1 (best): **human_hcd_tryp_best.msp.tar.gz** \\ (high-quality spectra, mostly tryptic peptides without \\ missed cleavages) \\ Library 2 (good): **human_hcd_tryp_good.msp.tar.gz** \\ (medium-quality spectra, mostly tryptic peptides \\ with missed cleavages) \\ Library 3 (semi-tryptic): **human_hcd_semitryp.msp.tar.gz** \\ (high- and medium-quality spectra, mostly \\ semi-tryptic peptides) | 646MB \\ \\ \\ 396MB \\ \\ \\ 599MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_best.msp.tar.gz|Download 1]] \\ \\ \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_good.msp.tar.gz|Download 2]] \\ \\ \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_semitryp.msp.tar.gz|Download 3]] |
^ //Libraries of selected spectra in NIST binary format. \\ 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:// ^
| Library 1 (best): **human_hcd_tryp_best.tar.gz** \\ Library 2 (good): **human_hcd_tryp_good.tar.gz** \\ Library 3 (semi-tryptic): **human_hcd_semitryp.tar.gz** | 1.5GB \\ 937MB \\ 1.4GB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_best.tar.gz|Download 1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_good.tar.gz|Download 2]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_semitryp.tar.gz|Download 3]] |
| **uniprot-all.fasta.tar.gz** - FASTA file used to create the library.| 7.0MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/uniprot-all.fasta.tar.gz|Download]] |
| **md5_checklist.chk** - MD5 hash file. | 1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/md5_checklist.chk|Download]] |
^ ^ Library 1^ Libraries 1,2^ Libraries 1,2,3^
|Total number of Spectra | 398,373| 598,850| 911,783|
|Unique Peptide Sequences | 257,122| 365,188| 605,677|
|Proteome Coverage | 27.9%| 32.2%| 35.3%|
----
===== Decoy Libraries (May 19, 2020) =====
The decoy library (sequence reversed) were 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.
^ Decoy Libraries - Description ^ Size ^ Link ^
^//Libraries 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://^
|Decoy for Library 1: **human_hcd_tryp_best_decoy.msp.tar.gz** \\ Decoy for Library 2: **human_hcd_tryp_good_decoy.msp.tar.gz** \\ Decoy for Library 3: **human_hcd_semitryp_decoy.msp.tar.gz**| 556MB \\ 352MB \\ 529MB | [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_best_decoy.msp.tar.gz|Download 1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_good_decoy.msp.tar.gz|Download 2]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_semitryp_decoy.msp.tar.gz|Download 3]]|
^//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://^
|Decoy for Library 1: **human_hcd_tryp_best_decoy.tar.gz** \\ Decoy for Library 2: **human_hcd_tryp_good_decoy.tar.gz** \\ Decoy for Library 3: **human_hcd_semitryp_decoy.tar.gz**| 1.5GB \\ 904MB \\ 1.4GB | [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_best_decoy.tar.gz|Download 1]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_good_decoy.tar.gz|Download 2]] \\ [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_semitryp_decoy.tar.gz|Download 3]]|
| **md5_checklist.chk** - MD5 hash file. | 1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/md5_checklist.chk|Download]] |
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