In CPLM database, we tried to make it powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service. For usage of local packages, please download the Manual. The CPLM 4.0 provide the search option and advance options.

1. Search. Five search options are provided, including substrate search, peptide search, advanced search, batch search and BLAST search.

(1) Substrate Search could be used to input one or multiple keywords (separated by space character) to search the CPLM database. The search fields including CPLM ID, UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias and Species.

Example: Please click on the "Example" button to search "Histone H3.1" in Protein Name field. By clicking on the "Submit" button, the related proteins will be shown.

(2) Advanced Search could be used to input two or more terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:

AND : the term following this operator has to be included in the specified field(s).
OR : either the preceding or the following term to this operator should occur in the specified field(s).
NOT : If selected, the term following this operator must be not contained in the specified field(s).

Example: You can click on the "Example" button to load an instance, which could search protein "Histone H3.1" in Homo sapiens. The human Histone H3.1 will be shown by clicking on the "Submit" button.

(3) Batch Search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt IDs to search the database. The list should be inputed as one keyword one line.

Example: You can click on the "Example" button to load three proteins UniProt accessions including P68431, A0PJT7, A5PLR1, P02295, P02296, P16106, Q6ISV8, Q6NWP8, Q6NWP9, Q6NXU4, Q71DJ3 and Q93081. By clicking on the "Submit" button, you can find "Histone H3.1".

(4) BLAST Search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined. The default parameters of E-value is 0.01.

Example: You can click on the "Example" button to load the protein sequence of Homo sapiens Histone H3.1. By clicking on the "Submit" button, you can find the related homologues.

2. Browse. Two simple ways have been provided for users to browse lysine modified protein in the database. Users can browse by species or by modification type. Type browse allows user to select interested type. Species browse allows user to choose interested species.

(1) Browse by species : You can select one of these species to browse all proteins with modified K-sites of corresponding species.

(2) Browse by Modification Types : You can select one of these modifications to browse all proteins with modified K-sites of corresponding modifications.

3. Localization probability (LP) score

The localization probability (LP) score was computationally assigned to each potential modified K-sites, based on the cumulative binomial distribution (Olsen, et al., 2006). LP scores range from 0 to 1, and a higher LP score represents a higher cumulative binomial probability for a site to be a real modification site (Olsen, et al., 2006). In this regard, as previously described (Humphrey, et al., 2013), we classified the modified K-sites in original peptides into four categories, including class I (>0.75), class II (≤0.75 and >0.5), class III (≤0.5 and ≥0.25), and class IV (<0.25), based on the pre-calculated LP scores.