PTM-Pro: Inhouseprotocols scripts

PTM-Pro
PTM-Pro 2.0

PTM-Pro

PTM-Pro: This program will fetch high confident PTM sites at peptide and protein level based on user-defined ptmRS probability cut-off. A summary of the number of PTM sites that qualify the said cut-off will be generated. Also, a PTM window consisting of 7 amino acids upstream and downstream of the PTM site will be provided. This window can be used for motif enrichment or to identify conserved motifs. Please read the following steps to prepare your input file and set up the analysis. sample file. Use: Database of RefSeq75 for executing sample file. (To save, "right click" and opt for "save link as").

Input file format: Text document (tab-delimited)

Order of columns:
First column - "Peptide sequence"
Second column - "Protein group accession"
Last column - "ptmRS probabilities"

Peptide Sequence	Master protein accession	. . .	ptmRS: Best Site probabilities
[R].sDIDSPPITAR.[N]	41327734	. . .	S5(Phospho): 99.56

Notes:
1. Please remove the rows where phosphoRS value is blank
2. There might be any number of columns in between the second and last columns. Arrangement of columns in this order is a MUST. The program may not work correctly if this order is not followed.

Select the organism:
Please select the appropriate organism. If the organism of your interest is not present in the drop down menu, write to us with subject lines as ptm-pro: database index.

Select the probability cut-off:
The default probability cut-off value is ≥75. You can change it as per your requirement.

Output file:
A zipped file is downloaded to your computer which contains the output file, a file containing a list of PTM peptides for which the PTM sites couldn't be fetched (ambigous PTM peptides) and a summary of your analysis. The output file is generated with a suffix of "_PTM.Site_PTM.Window_mmddyy.txt". An example output file is provided for your understanding. Download sample file (To save, right click and opt for "save link as").

Citing PTM-Pro:
1). In oral presentations, include attribution to "PTM-Pro, www.ptm-pro.inhouseprotocols.com" on pages that include information to PTM-Pro.
2). Please add to your manuscript the following sentence (typically in the "Methods" section): "High-confidence PTMs were profiled using PTM-Pro tool (Patil et al., 2018 )".

Process your data here

If you wish to email the results, then provide the correct Email ID below:

Select the organism:

Select the probability cutoff:

Select dbPTM (release year - 2019):

Patil, A. H., Datta, K. K., et al., Dissecting Candida pathobiology: Post-translational modifications on the Candida tropicalis proteome. 2018. OMICS: A Journal of Integrative Biology. 22, 544-552. [PubMed]

PTM-Pro

Input file format: Text document (tab-delimited)

Order of columns:
First column - "Peptide sequence"
Second column - "Protein group accession"
Last column - "ptmRS probabilities"

Peptide Sequence	Master protein accession	. . .	ptmRS: Best Site probabilities
[R].sDIDSPPITAR.[N]	41327734	. . .	S5(Phospho): 99.56

Select the organism:
Please select the appropriate organism. If the organism of your interest is not present in the drop down menu, write to us with subject lines as ptm-pro: database index.

Select the probability cut-off:
The default probability cut-off value is ≥75. You can change it as per your requirement.

PTM-Pro2.0

Version 2.0: The upgrade functionalities of PTM-Pro2.0 has come-up with several advanced features like graphical representation of summary of the data. Genereate statstically significant sequence motifs and compare the modifications with the literature evidence from dbPTM.

Process your data here

If you wish to email the results, then provide the correct Email ID below:

Select the organism:

Select the probability cutoff:

Select dbPTM (release year - 2019):

intensity-Based Absolute Quantification (iBAQ)

Protein Quantitation: The online scripts computes iBAQ values for the list of proteins provided by the user. Label-free quantification (LFQ) with iBAQ is calculated as: Sum of all peptide intensities divided by the number of theoretically observable tryptic peptides of a protein. The input file should be tab-delimeted text format. PSM table should be provided as input file and formated as shown below. Output file is generated and a suffix of "_quant_MMDDYY.txt" is appended to your input file name which will be downloaded to the local system.

Annotated Sequence

Gene Symbol

First Scan

Intensity

Process your data here

Select the organism:

distributed Normalized Spectral Abundance Factor (dNSAF)

dNSAF: The online scripts computes dNSAF values for the list of proteins provided by the user. Label-free quantification (LFQ) with dNSAF is calculated as: Peptides/spectral counts that are shared between proteins are distributed to each protein based on the amount of unique peptides/spectral counts found for each protein. Explanation is adapted from Washburn lab & Proteomics Center.

dNSAF

Shared spectral counts (sSpC_i) are distributed based on spectral counts unique to each protein i (uSpC_i) divided by the sum of all unique spectral counts for the M protein isoforms that shared peptide j with protein i, normalized against protein i's length (Length_i). Original publication: Zhang Y et al., (2010). Analytical Chemistry. 82:2272-2281. [PubMed]
The input file should be tab-delimeted text format. Peptide table should be provided as input file and formated as shown below. Output file is generated and a suffix of "_dNSAF_MMDDYY.txt" is appended to your input file name which will be downloaded to the local system.

Annotated Sequence

PSM count

Master Protein Accessions

Process your data here

Select the organism:

Patil, A. H., Datta, K. K., et al., Dissecting Candida pathobiology: Post-translational modifications on the Candida tropicalis proteome. 2018. OMICS: A Journal of Integrative Biology. 22, 544-552. [PubMed]

PTM-Pro: Post translational modifications - profiling