peptidew:lib:humanhcd20160503

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 download (447.36 KiB).
The meaning of the fields present in the comments of the library spectra can be found here (111.13 KiB).

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
Download 1


Download 2


Download 3
Libraries of selected spectra in NIST binary format.
The folders generated by extracting these packages
can be used directly by 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
Download 1
Download 2
Download 3
uniprot-all.fasta.tar.gz - FASTA file used to create the library. 7.0MB Download
md5_checklist.chk - MD5 hash file. 1KB 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
Download 1
Download 2
Download 3
Library of decoy spectra in NIST binary format (two parts).
The folders generated by extracting these packages
can be used directly by 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
Download 1
Download 2
Download 3
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/humanhcd20160503.txt · Last modified: 2020/11/20 16:22 (external edit)

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