update references

Author: Jhsmit

README.rst

@@ -22,20 +22,23 @@ Python package for HDX intrinsic exchange rate calculation.
 
 The calculations are based on the following papers:
 
+'Englander xls sheets' papers:
   Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. Primary structure effects on peptide group hydrogen exchange. `Proteins Structure, Function, and Bioinformatics <https://doi.org/10.1002/prot.340170110>`__ 17, 75–86 (1993)
 
   Connelly, G. P., Bai, Y., Jeng, M.-F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. `Proteins <http://doi.wiley.com/10.1002/prot.340170111>`__ 17, 87–92 (1993).
 
-
   Mori, S., Zijl, P. C. M. van & Shortle, D. Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. `Proteins Structure, Function, and Bioinformatics <https://doi.org/10.1002/(SICI)1097-0134(199707)28:3%3C325::AID-PROT3%3E3.0.CO;2-B>`__ 28, 325–332 (1997)
 
   Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. `J. Am. Soc. Mass Spectrom.  <https://doi.org/10.1007/s13361-018-2021-z>`__ 29, 1936–1939 (2018).
 
-..
-   1.Rubinson, K. A. Practical corrections for p(H,D) measurements in mixed H 2 O/D 2 O biological buffers. Anal. Methods 9, 2744–2750 (2017).
+'3ala' reference data:
+   Stofella, M.; Seetaloo, N.; St John, A. N.; Paci, E.; Phillips, J. J.; Sobott, F. Recalibrating Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry. Anal. Chem.  97 (5), 2648–2657 (2025).
+
+pH correction:
+   Rubinson, K. A. Practical corrections for p(H,D) measurements in mixed H 2 O/D 2 O biological buffers. Anal. Methods 9, 2744–2750 (2017).
 
 
-See also the excel sheet on the Englander group website: http://hx2.med.upenn.edu/download.html
+See also the excel sheets on the Englander group website: http://hx2.med.upenn.edu/download.html
 
 
 * Free software: GNU General Public License v3

hdxrate/hdxrate.py

@@ -227,6 +227,9 @@ def k_int_from_sequence(
        Function, and Bioinformatics 28, 325–332 (1997).
     .. [4] Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference Parameters for Protein Hydrogen
        Exchange Rates. J. Am. Soc. Mass Spectrom. 29, 1936–1939 (2018).
+    .. [5] Stofella, M.; Seetaloo, N.; St John, A. N.; Paci, E.; Phillips, J. J.; Sobott, F. Recalibrating
+       Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry. Anal. Chem.  97 (5), 2648–2657 (2025).
+
     """
 
     if len(sequence) < 3: