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                   README for CSPA_spectral_libraries
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Content:
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- README.txt file
- Folder A
	- CSPAhuman_filtered_M_pD.pepidx
	- CSPAhuman_filtered_M_pD.spidx
	- CSPAhuman_filtered_M_pD.splib
- Folder B
	- CSPAhuman_filtered_M_unmod_pD.pepidx
	- CSPAhuman_filtered_M_unmod_pD.spidx
	- CSPAhuman_filtered_M_unmod_pD.splib


Description:
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Folder A:
This folder contains the necessary spectral library filesfor perfoming a successful peptide
identification search with a .mzXML file.
The spectral library is filtered to high confidence and putative cell surface proteins 
within the CSPA. All methionine containing peptides are present as unmodified and 
with a oxidized methionine. All cysteine are carbamidomethylated. Deamidation of 
asparagine was left as originally identified.
An equal number of decoy spectra to real spectra was appended.

Folder B:
This folder contains the same spectral library as S1, except that all asparagines 
are unmodified.

File descriptions:
*.splib = spectral library itself, binary (machine-readable) format
*.sptxt = text (human-readable) version of the library file *.splib
*.spidx = indices on the precursor m/z value
*.pepidx = indices on the and peptide


Additional information:
-----------------------

Please refer to Lam et al. (2007, Proteomics), Lam et al. (2008, Nature Methods), 
Lam et al. (2010, Journal of Proteome research) and to the following link
http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Importing_Existing_Libraries
for detailed instructions how to use spectral libraries.

