ProteinCenter User Manual

**Table of Contents**

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.

**Header title**indicates the name by which a certain type of supplementary data is identified, in the import processes as well as in the export outputs**Short Name**is the abbreviated header used to refer to this supplementary data type, most commonly applied in the user interface in places with limited space**Data Type**specifies what kind of data the supplementary data represents**Description**contains a short description of the supplementary data and its interpretation. If a more elaborate explanation is warranted, this field will refer to a sub-section below

**Table B.1. Protein supplementary data**

Header Title | Short Name | Data Type | Description |
---|---|---|---|

Identification | |||

PP | PP | Probability | Probability for the identification of the protein |

XTANDEM_EVAL | EVAL | E-value | XTandem expectation value for the identification of the protein (log10) |

OMSSA_EVAL | EVAL | E-value | OMSSA expectation value the identification of the protein |

MASCOT_SCORE | MASCOTS | Score | Mascot score for the protein |

PHENYX_SCORE | PHENYXS | Score | Phenyx score for the protein |

PLGS_SCORE | PLGSS | Score | ProteinLynx Global Server score for the protein |

SPECTRUMMILL_ SCORE | SPECMS | Score | Spectrum Mill score for the protein |

SCORED_PEAK_ INTENSITY | SPI | Score | Percentage of the MS/MS peak-detected spectral ion current explained by the Spectrum Mill search interpretation |

UI | UI | String | Unambiguous identification of the protein |

IS | IS | String | A sub-group within an indistinguishable protein group that share the exact same peptides |

Quantitation | |||

EMPAI | IemPAI | Decimal number | Exponentially Modified Protein Abundance Index (imported), estimating absolute protein amount using the number of sequenced peptides per protein |

EMPAI_CALC | emPAI | Decimal number | As above, but calculated by ProteinCenter using the procedure described in Section B.1.1, “Calculated emPAI” below |

ITRAQ_4_RATIO_### | QR# | Ratio | iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117) |

ITRAQ_4_SD_### | QSD# | Standard deviation | Standard deviation on iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117) |

ITRAQ_4_EF_### | QEF# | Error factor | Standard error factor for iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117) |

ITRAQ_4_PVAL_### | QPV# | P-value | P-value for iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117) |

ITRAQ_4_N_### | QN# | Count | Number of peptides for iTRAQ 4-plex ratio (### denotes reporter ion 114, 115, 116 or 117) |

ITRAQ_8_RATIO_### | QR# | Ratio | iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121) |

ITRAQ_8_SD_### | QSD# | Standard deviation | Standard deviation on iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121) |

ITRAQ_8_EF_### | QEF# | Error factor | Standard error factor for iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121) |

ITRAQ_8_PVAL_### | QPV# | P-value | P-value for iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121) |

ITRAQ_8_N_### | QN# | Count | Number of peptides for iTRAQ 8-plex ratio (### denotes reporter ion 113, 114, 115, 116, 117, 118, 119 or 121) |

TMT_2_RATIO_### | QR# | Ratio | TMT 2-plex ratio (### denotes reporter ion 126 or 127) |

TMT_2_SD_### | QSD# | Standard deviation | Standard deviation on TMT 2-plex ratio (### denotes reporter ion 126 or 127) |

TMT_2_PVAL_### | QPV# | P-value | P-value for TMT 2-plex ratio (### denotes reporter ion 126 or 127) |

TMT_2_N_### | QN# | Count | Number of peptides for TMT 2-plex ratio (### denotes reporter ion 126 or 127) |

TMT_6_RATIO_### | QR# | Ratio | TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131) |

TMT_6_SD_### | QSD# | Standard deviation | Standard deviation on TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131) |

TMT_6_PVAL_### | QPV# | P-value | P-value for TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131) |

TMT_6_N_### | QN# | Count | Number of peptides for TMT 6-plex ratio (### denotes reporter ion 126, 127, 128, 129, 130 or 131) |

SILAC_RATIO_# | QR# | Ratio | SILAC ratio (# denotes isotope 1 through 9) |

SILAC_SD_# | QSD# | Standard deviation | Standard deviation on SILAC ratio (# denotes isotope 1 through 9) |

AQR | AQR | Ratio | Average Quantitative Ratio for a protein |

AQR# | AQR# | Ratio | Average Quantitative Ratio for a protein in a series (# denotes number 1 through 19) |

QSD | QSD | Standard deviation | Standard deviation for average quantitative ratio |

QSD# | QSD# | Standard deviation | Standard deviation for average quantitative ratio in a series (# denotes number 1 through 19) |

QSE | QSE | Standard error | Standard error for average quantitative ratio |

QSE# | QSE# | Standard error | Standard error for average quantitative ratio in a series (# denotes number 1 through 19) |

QPV | QPV | P-value | P-value for average quantitative ratio |

QPV# | QPV# | P-value | P-value for average quantitative ratio in a series (# denotes number 1 through 19) |

NPEP | NPEP | Count | Number of peptides observed for the protein |

NPEP# | NPEP# | Count | Number of peptides observed for the protein in a series (# denotes number 1 through 19) |

Generic Data | |||

GI# | GI# | Integer | Integer for generic use (# denotes number in range 1-9) |

GD# | GD# | Decimal number | Decimal number for generic use (# denotes number in range 1-9) |

GS# | GS# | String | String for generic use (# denotes number in range 1-9) |

L# | L# | URL link | Link for generic use, e.g. to an external webpage, database or file (# denotes number in range 1-9) |

Properties | |||

PTM | PTM | String list | All Post Translational Modifications associated with the protein |

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.

Peptide supplementary data are prepended by "`PEPTIDE_`

" in importers, to distinguish them from protein counterparts.

**Table B.3. Peptide supplementary data**

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