PROTEOMICA - User contributions [en]

DataGrid information in QuiXoT

2016-06-15T18:53:11Z

Pnavarro:

The DataGrid of [[QuiXoT]] contains different columns, according to the quantitation 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 quantitation 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)
:'''Psp''': Probability that a scan is an outlier with respect to the corresponding average
:'''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)
:'''Ppq''': Probability that a peptide is outlier with respect to the corresponding average
:'''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

[[Category:QuiXoT]]
[[Category:useful information]]

DataGrid information in QuiXoT

2016-06-15T18:52:51Z

Pnavarro:

The DataGrid of [[QuiXoT]] contains different columns, according to the quantitation 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.

test -- remove this.

Here is a list of the standard columns used in most quantitation 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)
:'''Psp''': Probability that a scan is an outlier with respect to the corresponding average
:'''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)
:'''Ppq''': Probability that a peptide is outlier with respect to the corresponding average
:'''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

[[Category:QuiXoT]]
[[Category:useful information]]

Main Page

2016-05-20T15:56:52Z

Pnavarro:

[[File:QuiXoT logo.png|300px|right]]

== Welcome to the QuiXoT Wiki! ==

=== What is QuiXoT? ===

{{main|QuiXoT}}

QuiXoT is a bioinformatic software developed especially to provide a tool for quantitative proteomics.

The latest stable release of the program is QuiXoT 1.4.00.

=== Why QuiXoT? ===

The tools available to the scientific community to quantitate and make statistical analyses in ''large scale'' quantitative proteomic experiments were very limited. For this reason we started developing QuiXoT in our laboratory.

In 2006 we started developing a tool for 18O isotope-labeling experiments able to automatically extract well assigned spectra, quantitate the data and make a fast statistical analysis. Everything within one hour.

Later, in February 2009, we decided to expand the software in order to analyze any type of isotopic labeling and to accept data from the most common mass-spectrometres.

=== Who is behind QuiXoT? ===

QuiXoT has been developed originally by '''[[User:pnavarro|Pedro Navarro]]''' and afterwards by '''[[User:Mtrevisan|Marco Trevisan-Herraz]]''', at the Cardiovascular Proteomics Lab of Prof. Jesús Vázquez, within the Centro Nacional de Investigaciones Cardiovasculares (CNIC), in Madrid, Spain (originally at the Protein Chemistry and Proteomics Lab, in the Centro de Biología Molecular Severo Ochoa, CBM-CSIC).

The [[:Image:QuiXoT logo.png|QuiXoT logo]] has been designed by José Pérez Pérez and Pedro Navarro.

=== References ===

* {{reference|authors = I. Jorge, P. Navarro, P. Martinez-Acedo, et al.|title = Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: Application to the study of VEGF-induced angiogenesis in endothelial cells|journal = Mol Cell Proteomics|year = 2009|DOI = 10.1074/mcp.M800260-MCP200}}

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