GPMAW lite – Protein Molecular Weight Calculator (and much more)

Protein calculator
Apr 10. 2017

Simple bioinformatics calculations on specific protein sequences

When working with proteins you often need to make simple bioinformatics calculations on a specific protein sequence.

  • What is the molecular weight of bovine serum albumin (BSA)?
  • How many N-glycosylation sites are present in my protein?
  • What peptides does trypsin cleavage generate?
  • What is the amino acid composition in my protein?

Questions like these are typical. Therefore, Alphalyse has launched GPMAW lite to facilitate these calculations. GPMAW lite is an online software for simple and easy bioinformatics calculations on protein amino acid sequences.


There are three different ways to enter a sequence into GPMAW lite;

1. Enter the known accession number from either NCBI or UNIPROT. The sequence will be retrieved into the sequence window automatically. With the NCBI and UniProt lookup function, you can easily find the accession number for any known protein from any organism.

2. Paste the sequence directly into the sequence window.

3. Type in the sequence using one letter AA code.


GPMAW lite functions

The cleanup function is useful, if your sequence contains numbers, spaces or lower case letters. When the protein sequence has been entered, you can perform a number of different bioinformatics analyses. Select the analysis you would like to have performed and click Calculate. At the top of the analysis results, the name and the sequence of the protein will be shown. You can use the Colorize function to highlight specific amino acids residues and potential N-glycosylations sites.

The Protein Information table provides all the basic information about your protein: Molecular Weight (mono-isotopic and average mass of non-reduced protein), theoretic calculated molar absorbance and extinction coefficient, isoelectric point, and hydrophobicity index.

The Amino Acid Composition function shows an amino acid composition table with numbers and percentage of individual amino acids. If the sequence contains any unusual amino acids it will also be visible in this table.

The protease Digest lists all peptides formed by theoretical complete digestion using the chosen protease. The table contains info about the peptide sequence, MH+ (mono-isotopic molecular weight of the protonated peptide in reduced form), isoelectric point pI and expected retention time in a HPLC run (reversed phase) for each peptide. You can sort all columns by clicking the header of the column to show peptides by position, HPLC retention time or by mass.


You can access GPMAW lite for free from any browser and computer, smartphone or tablet at our website.

Check out GPMAW lite  >>

About Alphalyse

Alphalyse uses expertise in the field of protein chemistry and bioinformatics, combined with top-of-the-line mass spectrometry equipment, to provide protein analysis services globally.

Alphalyse aims to deliver high quality data and customer service to all of our clients in a fast and convenient way.

Newsletter Subscribe to The Alphalyse Newsletter and get more
information on protein analysis methods and applications
© 2019 Alphalyse, Inc.