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peptidew:lib:phoshopept_labelfree_20190214 [2019/02/15 09:54]
 peptidew:lib:phoshopept_labelfree_20190214 [2021/07/08 00:45] (current)
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 +====== Human Phosphopeptide Label Free Library ======
 +===== Peptide Library (Feb. 14, 2019) =====
  
 +The human phosphopeptide 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 PXD000612.
 +
 +**Sharma K, D'Souza RC, Tyanova S, Schaab C, Wiśniewski JR, Cox J, Mann M.** //Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling.// Cell Rep. 2014 Aug 20. pii: S2211-1247(14)00620-2 PubMed: 25159151
 + \\
 +
 +
 +<WRAP center group 95%>
 +^ File - Description ^ Size ^ Link ^
 +| **human_hcd_labelfree_phospho_selected_passed.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. |  240MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2019_02_14/human_hcd_labelfree_phospho_selected_passed.msp.tar.gz|Download]] |
 +| **human_hcd_labelfree_phospho_selected_passed.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. |  540MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2019_02_14/human_hcd_labelfree_phospho_selected_passed.tar.gz|Download]] | 
 +| **uniprot-all.fasta.tar.gz** \\ FASTA file used to search CompRef human-mouse xenograft samples.|  7MB|[[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2019_02_14/uniprot-all.fasta.tar.gz|Download]]|
 +| **md5_checklist.chk** - MD5 hash file. |  1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2019_02_14/md5_checklist.chk|Download]] |
 + 
 +</WRAP>
 +
 +  * Total number of Spectra: **66,922**
 +  * Unique Peptide Sequences: **27,400**
 +  * Total Proteins in FASTA file used: **20,183**
 +  * Proteome Sequence Coverage: **3.9%**
 +
 +
 +===== 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 95%>
 +^ File - Description ^ Size ^ Link ^
 +| **human_hcd_labelfree_phospho_selected_passed_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. |  234MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_Phospho/human_hcd_labelfree_phospho_selected_passed_decoy.msp.tar.gz|Download]] |
 +| **human_hcd_labelfree_phospho_selected_passed_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. |  523MB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_Phospho/human_hcd_labelfree_phospho_selected_passed_decoy.tar.gz|Download]] | 
 +| **md5_checklist.chk** - MD5 hash file. |  1KB| [[https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/decoy/Orbitrap-HCD_Phospho/md5_checklist.chk|Download]] |
 + 
 +</WRAP>
 +
 +{{page>pepcopyright}}

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