Previously, we developed the qPhos database to host the quantitative phosphoproteome data in Homo sapiens, here we update it to qPTM database for 6 types of PTMs including acetylation, glycosylation, methylation, phosphorylation, SUMOylation, ubiquitylation in 4 different organisms including human, mouse, rat and yeast. Also, the matched proteome datasets were integrated if available. In total, 11,482,533 quantification events for 660,030 sites on 40,728 proteins under 2,596 conditions are collected and integrated in the qPTM database.

Quick Search

In the home page of qPTM, users can specify one field or all the fields to perform a quick search with the keyword(s) in the field(s). Users can simply click example and submit buttons to perform an example search.

Browse

In the Browse page, users can click one term to search the specified data in qPTM. The data was firstly grouped by organisms and further grouped by PMTs, the detailed information is consisting of three modules including conditions, samples and genes, which are sorted alphabetically. Users can click the initial and select the term of interest.

Advanced Search

In the Search page, users can add more keyword boxes and choose 'AND', 'OR' or 'NOT' to perform a more accurate multiple keywords search. Users can simply click example and submit buttons to perform an example search.

Result

In the Result page, users can view the search or browse results, and further filter them by the options we provide. More information about experiment and protein is also displayed while users click the 'Detail' button.

Reliability

To assess the reliability of the PTM sites, we developed a five-star scoring system through integrating the raw MS data-based FDR control and the recurrences of identification among datasets.

We performed the MS searching using MaxQuant 1.6.14 (MQ) against the UniProt database (Release 2021_01). The default values were used for all parameters unless stated otherwise, including 1% PSM FDR and 1% site-level FDR. The identified PTMs and relevant site-level FDRs were annotated to the curated data as re-identified FDR to enhance the reliability of qPTM.

For the datasets without raw MS data, the reliability of the PTM sites could be assessed through the recurrences of identification among datasets, which were characterized by three major standards in the five-star scoring system as follows:

1. The occurrences of the PTM site in qPTM database. We counted the identified times of each modified site in all datasets. Because the sites were filtered through a cutoff of site-level FDR <1% according to the literature, the more it was identified, the more it was reliable. Thus, modified sites were given zero points when identified once, one point when identified twice, and so on. The identified score was no more than 4 for each site.
2. The data reliability in the proteomics study. The posterior error probability (PEP) and localization probability data of each modified site were curated from the datasets if available. PEP, the probability that observed PSM is uncorrected, was under 1% while the localization probability higher than 75% was considered as high confident sites. The PTM sites that meet the criterion were given a point.
3. The occurrences of the PTM site in other classical PTM databases. Modified sites collected in dbPTM or PhosphoSitePlus were also given a point.

Taken together, the five-star scoring system assigned each PTM site with the reliability of 0-5 bright star(s) according to its recurrences of identification among datasets, and red bordered the bright star(s) if it has a site-level FDR < 0.01 according to the raw MS data-based re-identification.