About LymPHOS

LymPHOS is a continuous evolving PhosphoProteome DataBase for human T-Lymphocytes created and maintained by the CSIC/UAB Proteomics Laboratory. And it's also a Web-Application that allows everyone to freely access all this information from the Internet.

It is possible to Search for proteins and for peptide sequences with phosphorylation sites (p-sites), or browse the entire database, where experimental data (commented mass spectra) will support every p-site assignment.
An accurate description of the experimental design can be found in the Experimental section.
More detailed information on the people at the CSIC/UAB Proteomics Laboratory behind this project can be obtained at the About section.

General Help and Hints:

Phospho-peptides and p-sites representation

At many places in LymPHOS Web-Application, phospho-peptides sequences, and p-sites positions can be found:

Phospho-peptide sequences are usually represented as UPPERCASE BLUE or UPPERCASE BLACK aminoacid letters.

While p-sites are represented as bold lowercase aminoacid letters inside a square of different colors, depending of the Q-Ascore (phosphorylation assignment confidence) of the p-site:

  • When the Q-Ascore of the p-site is greater than the fixed threshold (19), the square is filled in green and has a red border, as in: s , t , y .

  • When the Q-Ascore of the p-site is lower or equal than the fixed threshold (19), the square is filled in orange and has a green border, as in: s , t , y .

This can be clearly seen in the following screen-shot of a Phospho-peptide View:

In this example, the phospho-peptide TDsREDEIsPPPPNPVVK has two p-sites; two phosphoriled serines:

  1. The first serine has a Q-Ascore (Q-Ascore 1 = 5.03) lower than the threshold (19), so it is displayed as s .
  2. The second serine has a Q-Ascore (Q-Ascore 2 = 40.32) greater than the threshold (19), so it is displayed as s .


Quantitative Summary View:

How to get to the Quantitave Summary of a phospho-peptide?

After you Search for Phospho-peptides, you can go directly to the Quantitative Summary of a peptide by clicking the green check-mark ( quantitative_yes ), located under the Quantitative Data Availability column ( quantitative_data ), that indicates the presence of quantitative information for that phospho-peptide.

From a Protein View, you can go to the Quantitative Summary of every of its Phospho-peptides supporting the phosphorilations found in that protein (sub-section Phosphorylations found and supporting MS Phospho-peptides). Only click the green check-mark ( quantitative_yes ), located under the Quantitative Data Availability column ( quantitative_data ), that indicates the presence of quantitative information for each phospho-peptide.

From a Phospho-peptide View, you can go to its Quantitative Summary by clicking the black scales icon ( quantitative_data ), located near the sequence of the phospho-peptide.


Quantitave Summary State

In the Quantitative Summary View of a phospho-peptide, you can see for every experimental condition its Quantitative State at every quantified activation time in that experimental condition.

The Quantitative State is represented in two different ways:

  1. Quantitative State as green and red arrows.

    The small arrows in parenthesis (down_regulated:: X, non_regulated:: Y, up_regulated:: Z) indicate:

    • down_regulated: : the number of spectra whose log2(ratio) is lower than under the mean log2(ratio) of its experiment normal distribution (and thus indicating a possible down-regulation).

    • down_regulated: : the number of spectra whose log2(ratio) is inside the range of the mean log2(ratio) ±  of its experiment normal distribution (and thus indicating a possible no change).

    • down_regulated: : the number of spectra whose log2(ratio) is greater than over the mean log2(ratio) of its experiment normal distribution (and thus indicating a possible up-regulation).

    While the big arrows show the trend, the summary of the possible changes indicated by the smalll arrows in parenthesis:

    •  Green-up arrows indicate a trend towards the up-regulation of that phospho-peptide.

    •  Red-down arrows indicate a trend towards the down-regulation of that phospho-peptide.

    •  Mixed Green-up and Red-down arrows indicate a trend towards no change of that phospho-peptide.

    The degree of filling of these big arrows shows the power of this trend: from an ambiguous trend, as an unfilled arrow; to a strong trend, as a fully filled arrow.

    Also, in the case of trends based only in one spectra, special shaded arrows (    ) are used, to warn the user.

  2. Quantitative State as numerical values.

    Below the arrows, for each quantified activation time in the experimental condition, the mean of the individual spectra normalized base 2 logarithms of the ratio between intensity at the indicated time and intensity at time 0 [ log2(ion intensity at time X / ion intensity at time 0) ], as well as the standard deviation of this mean, are shown, as calculated by the LymPHOS PQuantifier program (PQuantifier results).

    An asterisk ( * ) is shown near PQuantifier values, if they represent a significant change according to a t-student test with a 95% significance.
    And two asterisks ( ** ) are shown, if PQuantifier values represent a significant change according to a t-student test with a 99% significance.

    When available, below the PQuantifier calculated values it will also appear the mean of the individual spectra normalized base 2 logarithms of the ratio between intensity at the indicated time and intensity at time 0 [ log2(ion intensity at time X / ion intensity at time 0) ], as calculated by the DanteR program (DanteR results).

    A plus sign ( + ) is shown near DanteR values, when they represent a significant change according to an ANOVA test with an adjusted p-value lower than 0.05.