peptidew:lib:kustersynselected20170530

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peptidew:lib:kustersynselected20170530 [2018/08/07 12:53]
peptidew:lib:kustersynselected20170530 [2020/02/25 15:08] (current)
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 +====== Human Synthetic Peptide Spectral Library ======
 +=====  Peptide Library (May 30, 2017) =====
 +
 +The human synthetic peptide spectral library was created from data deposited with the ProteomeXchange Consortium (http://​proteomecentral.proteomexchange.org) via the PRIDE partner repository with the data set identifier PXD004732.
 +
 +Reference: D. Zolg … B. Kuster, Nature Methods, 14, 259 (2017): “Building ProteomeTools based on a complete synthetic human proteome”
 +
 +{{page>​peptidew:​lib:​newfiles_warning}}
 +
 +<WRAP center group 80%>
 +^ File - Description ^ Size ^ Link ^
 +| **human_synthetic_hcd_selected.msp.tar.gz** \\ Library 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. |  2.2GB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2017_05_30/​human_synthetic_hcd_selected.msp.tar.gz|Download]] |
 +| **human_synthetic_hcd_selected.tar.gz** \\ The Library of selected 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| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2017_05_30/​human_synthetic_hcd_selected.tar.gz|Download]] | 
 +| **uniprot-all.fasta.tar.gz** \\ FASTA file used to create the library.| ​ 7.2MB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2017_05_30/​uniprot-all.fasta.tar.gz|Download]] | 
 +| **md5_checklist.chk** - MD5 hash file. |  1KB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2017_05_30/​md5_checklist.chk|Download]] | 
 +</​WRAP>​
 +
 +  * Total number of Spectra: **696,692**
 +  * Unique Peptide Sequences: **188,805**
 +  * Total Proteins in FASTA file used: **20,183**
 +  * Proteome Sequence Coverage: **20.63%**
 +
 +
 +=====  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 80%>
 +^ File - Description ^ Size ^ Link ^
 +| **human_synthetic_hcd_selected_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,​ like Skyline, after unzipping. |  2.2GB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap_Fusion_Lumos-HCD_synthetic/​human_synthetic_hcd_selected_decoy.msp.tar.gz|Download]] |
 +| **human_synthetic_hcd_selected_decoy.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. |  4.6GB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap_Fusion_Lumos-HCD_synthetic/​human_synthetic_hcd_selected_decoy.tar.gz|Download]] | 
 +| **md5_checklist.chk** - MD5 hash file. |  1KB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap_Fusion_Lumos-HCD_synthetic/​md5_checklist.chk|Download]] | 
 +</​WRAP>​
 +
 +
 +{{page>​pepcopyright}}
 +
 +