delta PPM valut in output of comet

[Yongbo Wang]

Hi, is anyone knows that where is the delta M [PPM] value in comet output? As I saw this value was reported in other search engine? Thank you! 

[Jimmy Eng]

Comet doesn't report the mass difference in ppm in any of its outputs but it's easy to calculate.  In the pep.xml format, there is a "massdiff" attribute that reports the mass difference and "calc_neutral_pep_mass" which is the theoretical neutral mass of the peptide.  To get delta M in PPM, you can derive it using: 1e6 * massdiff / calc_neutral_pep_mass

In the text output, there are columns for the measured neutral mass (exp_neutral_mass) and the calculated neutral mass (calc_neutral_mass).  So you can derive delta M in PPM using:  1e6 * (exp_neutral_mass - calc_neutral_mass ) / calc_neutral_mass

[Yongbo Wang]

Thank you Jimmy, I get it now~

在 2015年10月8日星期四 UTC-7下午2:43:32，Jimmy Eng写道：

[Yongbo Wang]

Hi Jimmy, I just calculated the delta M, however I found that this value ranged from -800 up to >3000, I know this value represent the difference of exp and calc psm, so the lower the better, however, this huge range makes me confused since all psms are within 5%FDR, here is an example：

scan

num

charge

exp_neutral_mass

calc_neutral_mass

evalue

xcorr

delta_cn

sp_score

ions_matched

ions_total

plain_peptide

peptide

modifications

19292

1

3

2492.379

2491.38323

9.39E-09

4.5801

0.7324

311.3

24

96

SGGTLVLVGLGSEMTTVPLLHAAIR

R.SGGTLVLVGLGSEMTTVPLLHAAIR.E

the delta M = 1000000 * (2492.379 - 2491.38323) / 2491.38323 = 399.685599553463.

so is there anything wrong in my calculation or understanding? would you please give me some advice?

Thank you!

在 2015年10月8日星期四 UTC-7下午2:43:32，Jimmy Eng写道：

Comet doesn't report the mass difference in ppm in any of its outputs but it's easy to calculate.  In the pep.xml format, there is a "massdiff" attribute that reports the mass difference and "calc_neutral_pep_mass" which is the theoretical neutral mass of the peptide.  To get delta M in PPM, you can derive it using: 1e6 * massdiff / calc_neutral_pep_mass

[Jimmy Eng]

A nearly 1 Da mass difference does correspond to a large PPM mass error.  You just need to be aware that you likely allowed C13 isotope offsets to be applied in the search (the isotope_error parameter).  If this is confusing or unclear, both the application of that parameter and what it means for the resultant mass errors, consider stepping back and gaining more basic understanding of the data before attempting to do any analysis.  I hope that statement doesn't come across as being negative; it really is meant to be constructive feedback because the questions you're asking do imply you're pretty new to processing this type of data.  Good luck. 

[Yongbo Wang]

Thank you Jimmy, I have learned a lot from your answers. yes, this is the first time I process with the ms data, and I feel it quite difficult for me. I try to understand each parameters, but I can't get clear information from google or papers, so I am sorry for raising such many simple questions. I will refer to the papers, books or google. Thank you very much for the patience! Wishes~

在 2015年10月9日星期五 UTC-7上午12:05:37，Jimmy Eng写道：

[Jimmy Eng]

Feel free to keep posting questions ... I'm not trying to discourage you at all.  I'm just a little worried that you're doing analysis when you're not ready to do this analysis which can lead to mistakes that you're not even aware you're making.  But if you have no other resources to help you, I'm happy to continue answering whatever questions I can.