spectraNSA_test: Test data set with spectral level profiles formatted for...

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Test data set with spectral level profiles formatted for protlocassign

Description

Test data set that is the output of the function proteinDataPrep applied to QuantPSM_test. Like QuantPSM_test it contains descriptive information and NSA profiles for all peptide-spectrum matches associated with all spectra of TLN1, TLN2, AIF1 and the proteins listed in "markerListJadot".' In addition, peptides names (amino acid sequences) are prepended by their associated protein name and there are unique protein and peptide numerical identifiers. Data from the TMT MS2 data, AT5 experiment; see Tannous et al.

Usage

data(spectraNSA_test)

Format

An object of class data.frame with 6696 rows and 16 columns.

Value

A test data frame with spectral level profiles

prot

protein name

peptide

protein::peptide

SpectrumId

identification label of spectrum

PeptidesStartPostionInProtein

number of start position

modification

peptide modification list

N

a numeric vector

M

a numeric vector

L1

a numeric vector

L2

a numeric vector

P

a numeric vector

S

a numeric vector

Nyc1

a numeric vector

Nyc2

a numeric vector

Nyc3

a numeric vector

protId

a numeric vector

pepId

a numeric vector

References

Tannous, A.; Boonen, M.; Zheng, H.; Zhao, C.; Germain, C. J.; Moore, D. F.; Sleat, D. E.; Jadot, M.; Lobel, P., Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res 2020, 19, (4), 1718-1730.

Examples

data(spectraNSA_test)
str(spectraNSA_test)

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.