ProteinCenter User Manual
Table of Contents

Appendix B. Supplementary Data

Table of Contents

B.1. Protein supplementary data
B.1.1. Calculated emPAI
B.2. Gene supplementary data
B.3. Peptide supplementary data

On top of the core data and annotation related to proteins, ProteinCenter supports import and handling of a wealth of supplementary data. These are divided into several types and categories, primarily depending on whether they pertain to a protein or a peptide, and whether they denote an identification, quantitative measure, or other type of annotation.

B.1. Protein supplementary data

Table B.1. Protein supplementary data

Header TitleShort NameData TypeDescription
Identification   
PPPPProbabilityProbability for the identification of the protein
XTANDEM_EVALEVALE-valueXTandem expectation value for the identification of the protein (log10)
OMSSA_EVALEVALE-valueOMSSA expectation value the identification of the protein
MASCOT_SCOREMASCOTSScoreMascot score for the protein
PHENYX_SCOREPHENYXSScorePhenyx score for the protein
PLGS_SCOREPLGSSScoreProteinLynx Global Server score for the protein

SPECTRUMMILL_ SCORE

SPECMSScoreSpectrum Mill score for the protein

SCORED_PEAK_ INTENSITY

SPIScorePercentage of the MS/MS peak-detected spectral ion current explained by the Spectrum Mill search interpretation
UIUIStringUnambiguous identification of the protein
ISISStringA sub-group within an indistinguishable protein group that share the exact same peptides
Quantitation   
EMPAIIemPAIDecimal numberExponentially Modified Protein Abundance Index (imported), estimating absolute protein amount using the number of sequenced peptides per protein
EMPAI_CALCemPAIDecimal numberAs above, but calculated by ProteinCenter using the procedure described in Section B.1.1, “Calculated emPAI” below
ITRAQ_4_RATIO_###QR#RatioiTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_4_SD_###QSD#Standard deviationStandard deviation on iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_4_EF_###QEF#Error factorStandard error factor for iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_4_PVAL_###QPV#P-valueP-value for iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_4_N_###QN#CountNumber of peptides for iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_8_RATIO_###QR#RatioiTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
ITRAQ_8_SD_###QSD#Standard deviationStandard deviation on iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
ITRAQ_8_EF_###QEF#Error factorStandard error factor for iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
ITRAQ_8_PVAL_###QPV#P-valueP-value for iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
ITRAQ_8_N_###QN#CountNumber of peptides for iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
TMT_2_RATIO_###QR#RatioTMT 2-plex ratio (### denotes reporter ion 126 or 127)
TMT_2_SD_###QSD#Standard deviationStandard deviation on TMT 2-plex ratio (### denotes reporter ion 126 or 127)
TMT_2_PVAL_###QPV#P-valueP-value for TMT 2-plex ratio (### denotes reporter ion 126 or 127)
TMT_2_N_###QN#CountNumber of peptides for TMT 2-plex ratio (### denotes reporter ion 126 or 127)
TMT_6_RATIO_###QR#RatioTMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131)
TMT_6_SD_###QSD#Standard deviationStandard deviation on TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131)
TMT_6_PVAL_###QPV#P-valueP-value for TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131)
TMT_6_N_###QN#CountNumber of peptides for TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131)
SILAC_RATIO_#QR#RatioSILAC ratio (# denotes isotope 1 through 9)
SILAC_SD_#QSD#Standard deviationStandard deviation on SILAC ratio (# denotes isotope 1 through 9)
AQRAQRRatioAverage Quantitative Ratio for a protein
AQR#AQR#RatioAverage Quantitative Ratio for a protein in a series (# denotes number 1 through 19)
QSDQSDStandard deviationStandard deviation for average quantitative ratio
QSD#QSD#Standard deviationStandard deviation for average quantitative ratio in a series (# denotes number 1 through 19)
QSEQSEStandard errorStandard error for average quantitative ratio
QSE#QSE#Standard errorStandard error for average quantitative ratio in a series (# denotes number 1 through 19)
QPVQPVP-valueP-value for average quantitative ratio
QPV#QPV#P-valueP-value for average quantitative ratio in a series (# denotes number 1 through 19)
NPEPNPEPCountNumber of peptides observed for the protein
NPEP#NPEP#CountNumber of peptides observed for the protein in a series (# denotes number 1 through 19)
Generic Data   
GI#GI#IntegerInteger for generic use (# denotes number in range 1-9)
GD#GD#Decimal numberDecimal number for generic use (# denotes number in range 1-9)
GS#GS#StringString for generic use (# denotes number in range 1-9)
L#L#URL linkLink for generic use, e.g. to an external webpage, database or file (# denotes number in range 1-9)
Properties   
PTMPTMString listAll Post Translational Modifications associated with the protein

B.1.1. Calculated emPAI

ProteinCenter calculates emPAI values using the formula defined in Ishihama et al, 2005, with the number of experimental ('observed') peptides being the number of unique tryptic peptide sequences for the protein, and the number of theoretical ('observable') peptides being the number of unique peptide sequences found by a theoretical tryptic digestion of the protein sequence. Before this calculation is carried out, the peptides are filtered, in effect only considering peptides with masses between 700 and 2800 Da. Any incompletely digested peptides are treated as if all peptides resulting from a perfect tryptic digestion of the peptide sequence are observed. Semi- or non-tryptic peptide sequences are considered as evidence of their corresponding full tryptic peptide, if the peptide sequence part passes the mass filter.

B.2. Gene supplementary data

Table B.2. Gene supplementary data

Header TitleShort NameData TypeDescription
IdentificationTBA//FIXME 

B.3. Peptide supplementary data

Peptide supplementary data are prepended by "PEPTIDE_" in importers, to distinguish them from protein counterparts.

Table B.3. Peptide supplementary data

Header TitleShort NameData TypeDescription
Identification   
INIT_PROBIPPProbabilityInitial peptide probability
NSPNSPCount (fraction)Number of sibling peptides
NSP_ADJ_PROBNSPPProbabilityPeptide probability modified by sibling peptides
XTANDEM_EVALEVALE-valueXTandem expectation value for the identification of the peptide
PHENYX_PVALPVALP-valuePhenyx p-value for the identification of the peptide
MASCOT_SCOREMASCOTSScoreMascot score for the peptide
MSQUANT_SCOREMSQSScoreMSQuant score for the peptide
SCORE_PLUS_MS3S+MS3ScoreMSQuant combined score of conventional Mascot score and MS3 score based on the most intense fragment ions

SPECTRUMMILL_ SCORE

SPECMSScoreSpectrum Mill score for the peptide

SCORED_PEAK_ INTENSITY

SPIScorePercentage of the MS/MS peak-detected spectral ion current explained by the Spectrum Mill search interpretation
Quantitation   
ITRAQ_4_RATIO_###QR#RatioiTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_4_EPCT_###%E#Relative erroriTRAQ 4-plex error percentage for ratio (### denotes reporter ion 114, 115, 116 or 117)
ITRAQ_8_RATIO_###QR#RatioiTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
ITRAQ_8_EPCT_###%E#Relative erroriTRAQ 8-plex error percentage for ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121)
TMT_2_RATIO_###QR#RatioTMT 2-plex ratio (### denotes reporter ion 126 or 127)
TMT_2_SD_###%E#Relative errorTMT 2-plex error percentage for ratio (### denotes reporter ion 126 or 127)
TMT_6_RATIO_###QR#RatioTMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131)
TMT_6_SD_###%E#Relative errorTMT 6-plex error percentage on ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131)
SILAC_RATIO_#QR#RatioSILAC ratio (# denotes isotope 1 through 9)
SILAC_SD_#QSD#Standard deviationStandard deviation on SILAC ratio (# denotes isotope 1 through 9)
AQRAQRRatioQuantitative Ratio for a peptide
AQR#AQR#RatioQuantitative Ratio for a peptide in a series (# denotes number 1 through 19)
QSDQSDStandard deviationStandard deviation for average quantitative ratio
QSD#QSD#Standard deviationStandard deviation for average quantitative ratio in a series (# denotes number 1 through 19)
QSEQSEStandard errorStandard error for quantitative ratio
QSE#QSE#Standard errorStandard error for quantitative ratio in a series (# denotes number 1 through 19)
QPVQPVP-valueP-value for average quantitative ratio
QPV#QPV#P-valueP-value for average quantitative ratio in a series (# denotes number 1 through 19)
Generic Data   
GI#GI#IntegerInteger for generic use (# denotes number in range 1-9)
GD#GD#Decimal numberDecimal number for generic use (# denotes number in range 1-9)
GS#GS#StringString for generic use (# denotes number in range 1-9)
L#L#URL linkLink for generic use, e.g. to an external webpage, database or file (# denotes number in range 1-9)
Properties   
PIPIDecimal numberThe predicted isoelectric point of the peptide, based on the sequence only (post-translational modifications are not taken into consideration)
GRAVYGRAVYDecimal numberGrand average of hydropathy, i.e. the sum of hydropathy values of all the amino acids in the sequence, divided by the number of residues