DataGrid information in QuiXoT

The DataGrid of QuiXoT contains different columns, according to the quantification strategy used, along with some user-defined options. Advanced users can modify the .xsd files in the configuration folder to change these columns according to their needs.

Here is a list of the standard columns used in most quantification methods:

FileName: MSF or SRF file containing SEQUEST identifications

RAWFileName: RAW file containing the mass spectra

Index: Identification number of the scan in increasing order of FDR (error rate of peptide identification)

spectrumIndex: Identification number of a spectrum to find its data in the binStack folder

FirstScan/LastScan: Number of the first and last scans in each raw file where the peptide was identified

Charge: Peptide’s ionization charge

FDR: False Discovery Rate with which a peptide was identified in the database from its MS/MS spectrum

FASTAshort: Truncated form of FASTAProteinDescription

FASTAProteinDescription: Description of the protein in FASTA database

Sequence: Amino acid sequence of the peptide (including all kind of modifications)

EqSequence: Amino acid sequence of the peptide taking into account that the different labeled forms belongs to the same peptide

pI: Theoretical Isoelectric Point of the peptide

PrecursorMass: Experimentally-determined molecular mass of the peptide (non-ionized form)

q_peptide_Mass: Theoretical molecular mass of the non-labeled form of the peptide (this is calculated during the quantification)

XC1D: Sequest Xcorr score of the best match

XC2D: Sequest Xcorr score of the second best match

deltaCn: Normalized difference between the first and second best scores

Sp: Sequest Sp parameter

SpRank: Sequest Sp-based ranking

Proteinswithpeptide: Number of additional proteins containing the peptide (and shown within the redundance table)

q_A: Amount of peptide in sample A

q_SD_A: Standard deviation of q_A

q_B: Amount of peptide in sample B

q_SD_B: Standard deviation of q_B

q_log2Ratio: Base 2 logarithm of A/B ratio

q_f: Labeling efficiency (18O labeling only)

q_SD_f: Standard deviation of f

q_Calibration: Mass shift (allows user to manually compensate for a systematic error in mass calibration)

q_DeltaMZ: Difference between theoretical and fitted m/z

q_Alpha: Leptokurtosis’ coefficient for peak fitting

q_SD_Alpha: Standard deviation of q_Alpha

q_Sigma: Peak half-width at 50% intensity

q_SD_Sigma: Standard deviation of q_Sigma

q_DeltaR: Mass increase introduced by labeling

q_Background: Fitted background signal

q_SQWindowsLeft: Mean squared deviation between experimental and theoretical spectra in a window at the left of the isotopic cluster

q_SQWindowsRight: Mean squared deviation between experimental and theoretical spectra in a window at the right of the isotopic cluster

q_SQPeptide: Mean squared deviation between experimental and theoretical spectra in a window spanning the isotopic cluster

q_windowRight: ??

q_SQTotal: Total Squared deviation between experimental and theoretical spectra

numLabel1: Allows the user to manually reject the spectra for statistics (1: used in statistics / 0: not used in statistics)

protLabel: Allows the user to consider the peptide as belonging to a different protein when performing the statistics

peptLabel: Allows the user to consider the scan as belonging to a different peptide when performing the statistics

DoubleFree1/2/3: Allows the user to introduce free text, numerical labels or to store the result of mathematical operations

Label4: Free field

Label5: Contains information about the reliability of Newton-Gauss fit method during the quantification process (Pedro: explicar las opciones)

dp_deployment:

st_Meth: Variable which informs whether a peptide contains methionines (1), oxidized methionines (2) or no methionines (0)

st_Cterm: Variable which informs if the last the peptide is tryptic (st_Cterm = 0) or not (st_Cterm = 1). Note that although originally this variable was intended to inform about C-terminus peptides, this is not always true (as C-terminus peptides ending with lysine or arginine will have st_Cterm = 0). However the name and the current definition is kept for practical reasons.

st_PartialDig: Variable which informs if the peptide has been partially digested (0: no partial digestion / 1: partially-digested peptide without a subpeptide identified / 2: subpeptide from a partially-digested peptide/ 3: partially-digested peptide with subpeptide identified)

st_excluded: Indicates that the scan has been excluded from statistics

Vs: Fitting weight of the scan

Xs: Base 2 logarithm of A/B ratio (corrected for 18O labeling efficiency)

SD_Xs: Standard Deviation of Xs

Xs_NoCorrf: Base 2 logarithm of A/B ratio (not corrected for 18O labeling efficiency)

Ws: Statistical weight of the scan

Zs: Standard normal value at scan level (Xs-Xp normalized to have a SD of one)

FDRs: False discovery rate at the scan level: proportion of scans expected to deviate by chance alone from peptide mean within the population of observed scan outliers (used to detect scan outliers)

Xp: Averaged log2ratio of the peptide

SD_Xp: Standard Deviation of Xp

Wp: Statistical weight of the peptide

Zp: Standard normal value at peptide level (Xp-Xq normalized to have a SD of one)

FDRp: False discovery rate at peptide level: proportion of peptides expected to deviate by chance alone from protein mean within the population of observed peptide outliers (used to detect peptide outliers)

Xq: Averaged log2ratio of the protein

SD_Xq: Standard Deviation of Xq

Wq: Statistical weight of the protein

Zq: Standard normal value at protein level (Xq-X normalized to have a SD of one)

Pq: Probability that a protein is outlier with respect to the corresponding average

FDRq: False discovery rate at the protein level: proportion of proteins expected to deviate by chance alone from the grand protein mean within the population of observed protein outliers (used to detect significant protein expression changes)

q_index: Identification number of each quantified protein

p_index: Identification number of each quantified peptide within its corresponding protein

s_index: Identification number of each quantified scan within its corresponding peptide

scan_per_peptide: Number of scans with which the peptide was quantified

pep_per_prot: Number of peptides with which the protein was quantified